"Mismatch extentref entry reference count"

[Killerbob]

I keep getting this error when I run First Aid on my "Master - Data" partition in Monterey. It shows up when First Aid checks snapshot 1, and the warning says:

Cross Check : Mismatch between extentref entry reference count (1) and calculated fsroot entry reference count (0) for extent (189321228 + 1)

First Aid then checks snapshot 2, and at the end of the disk check First Aid says:

The volume /dev/rdisk3s1 was found to be corrupt and needs to be repaired.
Performing deferred repairs
The volume /dev/rdisk3s1 appears to be OK
File system check exit code is 0
Restoring the original state found as mounted
Operation successful

I also tried running First Aid from boot recovery, and the same thing happens.

Every time I run First Aid, I get this message... How do I fix this?

 

[bogdanw]

Have you tried running First Aid on the physical disk?
Preferably from Recovery - Show All Devices - click on the disk instead of the container and then on First Aid.
https://support.apple.com/guide/disk-utility/repair-a-storage-device-dskutl1040/21.0/mac/12.0
Of course, backup your important data first, just in case

 

[Killerbob]

I just ran First Aid from boot again. The results were:

Master (volumes): no issues
Master: no issues
Master - Data: snapshot 1 of 16 warning: Cross Check : Mismatch between extentref entry reference count (1) and calculated fsroot entry reference count (0) for extent (189321228 + 1)
snapshot 2 of 16, 3 of 16, etc.: no issues

Why the heck is First Aid not fixing the issue?

 

[bogdanw]

Sometimes, even from recovery, Disk Utility forgets to unmount volumes before performing First Aid and returns false errors. From recovery, I always unmount all the volumes of the drive, then run First Aid.

You can also try from Terminal:
diskutil list physical
diskutil unmountDisk /dev/disk1
diskutil verifyDisk /dev/disk1
diskutil repairDisk /dev/disk1 (only necessary if errors are reported by the verify command)
fsck_apfs /dev/disk1

fsck_apfs can be run with -n verify only, -y "always repair, -o "repair overallocations; please do not run an older fsck_apfs on newer systems with this option"

 

[Killerbob]

I disabled Time Machine, and then blew away ALL local snapshots, using Terminal.

Booting into Recovery and using Disk Utilities, I then ran First Aid on all instances of my Master drive, and all is now well. Of course there are no snapshots to show the mismatch against.

I will let the system run for a day or so, and see if First Aid coughs up any issues.

 

[vr_driver]

I disabled Time Machine, and then blew away ALL local snapshots, using Terminal.

Booting into Recovery and using Disk Utilities, I then ran First Aid on all instances of my Master drive, and all is now well. Of course there are no snapshots to show the mismatch against.

I will let the system run for a day or so, and see if First Aid coughs up any issues.

Hi killerbob. Have you had any issues since blasting all the time machine snapshots? I’m having the same issue, except I’m on big sur, with my macmini. Only started yesterday.

 

[Killerbob]

No issues since then...

 

[marko566]

I have exactly the Same Problem. If i do a Backup on my external HDD then the created snapshot has the Problem in the First aus:
Only Snapshot 8 and 9 to the external disc has the Problem. All other on the installed ssd are working Fine.
any idea. I don´t want to reinstall my mac

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warning: mismatch between extentref entry reference count (0) and calculated fsroot entry reference count (-1) for extent (259529832 + 8)

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error: mismatch between extentref entry reference count (-1) and calculated fsroot entry reference count (0) for extent (259529832 + 8)

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[bogdanw]

Only Snapshot 8 and 9 to the external disc has the Problem. All other on the installed ssd are working Fine.

You could delete those snapshots.
Apple - View APFS snapshots in Disk Utility on Mac - Delete an APFS snapshot
https://support.apple.com/guide/disk-utility/view-apfs-snapshots-dskuf82354dc/mac

 

[marko566]

Yes but after some backups it comes back. This can not be. Is my SSD broken?

 

[bogdanw]

Is my SSD broken?

Try SSDReporter, it's free https://www.corecode.io/ssdreporter/index.html

 

[Marx55]

Can be fixed running First Aid on the top container instead of the volume, as First Aid suggests to do (read its small print).

 

[joshuawagner]

Thank you! This worked for me!
For the record, I forgot to check if the disk was unmounted, but I did make sure to run first aid on the container. I didn't delete any time machine snapshots, even though there was one that was giving the same sort of error.
I also ran across a cli-based APFS disk evaluation tool called smartmon tools `brew install smartmontools`

 

[CuteBaby]

No issues since then...

Is this even after re-enabling Time Machine, or have you left Time Machine permanently disabled?

 

[Killerbob]

Is this even after re-enabling Time Machine, or have you left Time Machine permanently disabled?

I actually had a few Time Capsules I used for Time Machine, and I never turned off Time Machine. This was well over a year ago though and on macOS Monterey. Most my Macs are now on Ventura and a few of them Sonoma - and I haven’t seen these errors for ages.

 

[CuteBaby]

I actually had a few Time Capsules I used for Time Machine, and I never turned off Time Machine. This was well over a year ago though and on macOS Monterey. Most my Macs are now on Ventura and a few of them Sonoma - and I haven’t seen these errors for ages.

Argh, didn't realize your original post was from that far back. Thanks for your reply!