You’ve just run First Aid in Disk Utility, or fsck_apfs, and that reports warnings or errors. What should you do next?

Failure to unmount

By far the most frequent error encountered in Disk Utility’s checks results from its inability to unmount a volume before it can start testing. While this is reported as an error, and it prevents the checks from running, it can sometimes be solved by manually unmounting the volume in question. It normally doesn’t indicate anything sinister, and is simply frustrating.

Repeat in Recovery mode

If the warnings or errors were reported on your current boot Data volume and you ran that check in normal user mode, consider starting your Mac up in Recovery mode to repeat the check there.

Although macOS does an impressive job of performing checks on a live volume, it’s more reliable and more likely to be able to perform any repairs needed in Recovery mode, when the Data volume isn’t mounted and live. When there, if you prefer, you can still use fsck_apfs in Terminal.

The other case where checks may be best made in Recovery are those on an active Time Machine backup volume. That’s because those can be difficult to unmount before running the checks, although that is possible as long as a backup isn’t being made at the time, or Spotlight indexing taking place. The sure way to avoid those is to do so in Recovery mode.

Warnings or errors?

Any remarks about problems or irregularities encountered during checks should make explicit whether they are warnings or errors, and it’s essential to make a clear distinction between them.

Warnings are observations that could have significance, or might be perfectly normal in the circumstances. Only an APFS engineer is likely to be able to tell the difference. Among the commonest are those reporting missing xattrs for compressed files:
warning: inode (id 113812826): Resource Fork xattr is missing for compressed file
Experience is that those aren’t related to any consequent errors, and you should be able to leave those alone.

Errors are abnormalities that do have more significance, and might have the potential to cause further problems. Where possible, First Aid or fsck_apfs should attempt to repair those, most probably by performing “deferred repairs”. Those are normally minor errors that it already has plans to attend to when that volume is next mounted, the time that APFS normally performs its routine maintenance.

Snapshots

These are read-only copies of the file system metadata at a previous instant in time, and are associated with retained storage blocks. They aren’t part of the active volume, and their metadata are separate. As they’re read-only, any warnings or errors are most unlikely to be fixed, so you have a choice of leaving that snapshot to be deleted routinely by age, or deleting it early yourself.

Snapshots are made by backup utilities including Time Machine, which are required by Apple to have a mechanism that will delete them automatically after a set period. In the case of Time Machine, that’s when the snapshot is over 24 hours old. Snapshots aren’t backups, but augment regular backups, and stand in for them when backup storage isn’t available. In general, there seems little point in deleting a snapshot early just because there’s a reported warning or error for it, as that won’t affect the health of the active volume.

Identifying faulty items

Warnings and errors related to specific files or directories are normally given with an item id, which should be their inode number. To go any further, you’ll need to convert that to a path and file/directory name. You should therefore copy and paste all reports into a separate file as reference. Resolving an inode to a path and item name is detailed in this article.

In many cases involving items that can be resolved to an existing path, the faulty item is in one of the hidden folders such as .Spotlight-V100 for Spotlight indexes, or .DocumentRevisions-V100 for the document version database. In the former, rebuilding Spotlight’s indexes may resolve the problem, but you’re unlikely to be able to do anything about the latter.

If the inode resolves to a regular file, deleting that can remove the problem, but when you try restoring that file from a backup you may discover the backup has the same problem. Getting to the bottom of a recurrent file system error might require the knowledge and skills of an Apple engineer. Consider reporting this using Feedback, as it should then help iron out any remaining bugs in APFS.

You should also consider whether your Mac might be running old third-party software that is causing recurrent errors. Normally, products should work at a higher level that isolates them from the file system itself, but there are some surprising exceptions. If you can identify a cause, please inform the developers of that software so that it can be fixed.

Old versions of APFS

One potentially dangerous practice occurs when an older version of APFS changes a newer file system. APFS back in High Sierra and Mojave knew nothing of boot volume groups, firmlinks, or many of the features of more modern versions of APFS. If you really must run different versions of macOS on the same Mac, or shared external storage, avoid such version conflicts, and never run an older version of Disk Utility or fsck_apfs on a newer APFS container or volume.

If you bought an M1 Mac with just a 256 GB internal SSD and have kept up with macOS upgrades and updates, should you be worried that it’s running out of space by the time it makes it to Tahoe? Dare you look at Storage settings to see how much of the SSD is now swallowed up by System Data? This article explains why macOS 26 shouldn’t devour the last of your SSD, and how you can ensure that it doesn’t.

What’s on your Mac’s internal SSD?

Internal boot disk layout is most complex in Apple silicon Macs, as theirs is divided into three partitions (or APFS containers). Two are hidden and contain pre-boot and other low-level support files, and amount to around 6 GB. The Macintosh HD partition then takes the lion’s share, the whole of the remainder. Even on a 256 GB SSD, that’s about 250 GB.

Volumes within Macintosh HD include:

• System, just over 12 GB,
• VM, varies in size according to how much virtual memory is swapped out to disk,
• Preboot, just under 8 GB,
• Recovery and others not normally mounted, a total of less than 2 GB,
• Data, whose size is determined by what you store there.

The system your Mac actually boots into isn’t the System volume itself, but a snapshot made of it, occupying the same space, plus a little extra for the snapshot’s metadata including its tree of hashes to form its seal and signature. Because this is a snapshot it uses the same data stored for the System volume, and doesn’t double that up.

This should allow your Data volume a maximum of 228 GB, less any space required by the VM volume. Although installation of a macOS upgrade or update will require substantial additional space, once that’s complete the space taken by the System volume and its snapshot should fall to little more than 12 GB.

What happens when macOS is upgraded?

In traditional macOS upgrades, the Installer app was downloaded first, and itself required around 13-15 GB. That was run, and expanded its contents to be installed onto the System volume, replacing much or all of it.

Updates work more economically, as they contain only the files that have changed, so far less than the Installer app. When they’re installed, they replace only those files changed in the System volume, ready for a new snapshot to be made from that, to be used to boot that Mac. So an update-style upgrade, as you should get when going from macOS 15.7 to 26.0, should require a much smaller download, a faster install, and less space to install the new version of macOS. However, the end result should be identical, with exactly the same files installed in the System volume, and exactly the same in the snapshot used when running.

Whichever is used, the installation process is similar. First, the files to be installed are expanded, then they’re written to the mounted System volume, with some going onto the Data volume as well. Once the System volume is complete, a snapshot is made of it, and that’s sealed using a tree hierarchy of hashes, culminating at the top of the tree in the seal.

What is System Data?

Storage settings scans the contents of the boot volume group, Macintosh HD, and divides the storage used into different categories like Applications and Podcasts. It appears to total those up and account for the remainder of storage used in the category System Data. That doesn’t include the size of the System volume, or its snapshot, but can include temporary files like caches, snapshots, and anything else it can’t account for in other categories.

Taking control

If there are substantial amounts of space that aren’t accounted for on your Mac’s internal SSD, and you want to reduce that, you need to account for it before deciding what to do about it.

First check for large snapshots. I hear repeatedly of Macs that turn out to have hundreds of GB being used by snapshots unnecessarily, and the current record is over 400 GB. The easiest place to check for those is in Disk Utility. In the sidebar on the left select the Data volume, then Show APFS Snapshots in the View menu for them to be displayed at the foot of the main view.

Backup utilities including Time Machine normally make a snapshot with each backup, and retain them for 24 hours, following which they’re automatically deleted. As snapshots can’t exclude folders in the way that Time Machine can in its backups, if you’ve been working with a couple of 100 GB VMs then they will be retained in snapshots even though you probably exclude them from being backed up.

Once you’re happy that free space isn’t being retained in snapshots, use a disk mapping utility like DaisyDisk or GrandPerspective to hunt down other large files and folders that you may not need. One reader here recently discovered that their iOS and iPadOS backups had taken over more than half the space on their Mac’s SSD.

Wait a day or two after upgrading

Installing a macOS upgrade also changes files on your Data volume, and may retain temporary support files. These are normally cleaned up in the next 24 hours, and you may be able to encourage that by starting your Mac up in Safe mode, leaving it a couple of minutes, then restarting it in normal user mode.

By a couple of days after the upgrade, your Mac should have returned to normal use of storage. If it hasn’t, check snapshots and go hunt that missing space.