This article explains how to deal with warnings and errors reported either when you run Disk Utility’s First Aid, or by the command tools fsck or fsck_apfs, on an APFS volume or container.

Keep a record

Even if the item is repaired successfully, it’s essential to keep a record of what happened. In Disk Utility, expand the First Aid window so you can see the full output of fsck_apfs, select its whole contents, copy and paste them into a text document, and save that. Do the same with the output in Terminal if that’s what you used.

You may also find two text log files of potential use: /var/log/fsck_apfs.log and /var/log/fsck_apfs_error.log, both accessible in Console or a text editor. Although errors may also be written to the Unified log, you’ll probably want to avoid going there.

Was this on the Data volume?

First Aid in Disk Utility will check and attempt to repair the current Data volume when running in normal user mode, by effectively freezing the Mac. However, that’s not as reliable as running the same procedure when your Mac is in Recovery mode. If you see warnings or errors reported from the current Data volume in normal user mode, before going any further start your Mac up in Recovery and repeat the checks in Disk Utility (or fsck_apfs) there, to confirm they are real, and give your Mac the best chance of making a successful repair.

This can also sometimes help when checking backup volumes, and any that have proved difficult to check because the volume can’t be unmounted in normal user mode.

Are these just warnings?

Read carefully through your copy of the output of fsck_apfs and check whether the comments there are warnings, or contain specific errors. Warnings aren’t uncommon, and are often of little consequence even when you can understand them. Among the commonest is
Resource Fork xattr is missing for compressed file
As there’s nothing you could or should do about that, keep the record and don’t worry about it.

You’ll occasionally see a report that “deferred repairs” were completed. These appear to be minor fixes that APFS keeps for a convenient moment. Provided they are fixed without further error, you should be able to ignore them safely.

If a line explicitly reports an error, and fsck_apfs was unable to repair it, then it’s something you should take more seriously, and try to pin down the site of the problem.

Identify the item

fsck_apfs identifies items with their inode number, an integer that can be very large. To make any sense of that, you need the volume number as well, and a means of converting the two into a path. My free utility Mints can do that in its inode Resolver window, from the Window/Data/Inode menu command, or you can do it yourself in Terminal with a command like
GetFileInfo /.vol/[volnumber]/[inode]
where volnumber is the volume number, and inode is the number given in the error or warning. This is explained in detail here.

Now that you know which file or folder resulted in the error or warning, you need to decide whether you can do anything about it. This is most important when you keep seeing similar errors, so you can prevent them from happening in the first place.

Is the item in a snapshot?

Checking snapshot 2 of 23 (com.apple.TimeMachine.2023-08-27-072736.local)
warning: inode (id 113812826): Resource Fork xattr is missing for compressed file

Snapshots are a special case, as they’re intended to be read-only, so are most unlikely to be repairable. If this is a snapshot on a volume that is backed up by Time Machine or another utility, then the only way you’ll fix this is by deleting that snapshot. Don’t do that, though, if the snapshot is on the volume storing your backups, as you’d be deleting one of those backups.

If this problem recurs in other snapshots, then it most probably reflects a problem in the file in the snapshot. Is it perhaps a large virtual machine (VM) or something similar? Keep your VMs on a separate volume which you exclude from backups, because of the many problems they can cause. The best way to back up a VM is when it’s shut down, as a simple copy to a separate backup storage volume. You can do the same with any other file that seems to be the cause of repeated problems in snapshots: move it to a separate volume that’s in Time Machine’s list of excluded items, and make arrangements for that volume to be backed up separately when the files aren’t in use.

Is the item in a Spotlight index?

Several of those who report repeated warnings or errors in APFS trace them to part of the Spotlight indexes on that volume, which are stored at the top level of all indexed volumes, in the hidden folder .Spotlight-V100. If that’s the case, your next move is to force those indexes to be rebuilt, in the hope that fixes the problem.

To do that, open Spotlight settings, and click the Search Privacy button at the foot of its window. Use the + tool to add the volume on which the problems have been occurring, then close those settings. Leave your Mac for a minute or so, open those settings again, select the volume you just added to the list, and use the – tool to remove it. In the next ten minutes or so, check Activity Monitor’s CPU window, where you should see high levels of activity from indexing processes such as mds and mds_stores, that confirm those indexes are being rebuilt.

Is the item in another special folder?

There are other hidden folders with special roles that appear on volumes and could be the source of APFS errors. These include .DocumentRevisions-V100, containing the document version database. If the problem file is inside that, there isn’t much you can do about it. It may be possible to delete the whole folder, but that will destroy all saved versions of documents on that volume.

It’s just a regular file

If the volfs path resolves to a regular file, then maybe deleting that file will stop the problem from recurring. Don’t expect a backup copy of that file to be any different, though, as any problem with that file could easily recur. 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.

Is your Mac running anything that might break files?

As a final thought, you should consider whether any third-party software might be the root cause of the problem. Normally, such 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.

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.