Given it’s built by the build-system I have not medled with the squashfs myself, the only hunch I have is that I have a custom prime step that adds a file. Could that cause issues like this?
It is probably the second error that is causing both problems:
Error:found errors in file output: unusual mode ‘rwsr-xr-x’ for entry ‘./bin/fusermount’, file type ‘c’ not allowed (./dev/fuse)
The resquash test is run as non-root, so when the snap is unsquashed, dev/fuse won’t be created and bin/fusermount will not have the setuid bit set, so when it is squashed and compared, dev/fuse is missing and bin/fusermount is 0755, so there is a checksum mismatch.
I suggest removing dev/fuse and bin/fusermount before mksquash (‘organize’ in your snapcraft.yaml can help with the bin/fusermount removal; you might have to play around with override-* to get rid of dev/fuse (@sergiusens may be able to help if you get stuck)).