I'm positive about Time Machine over AFP. iSCSI was indeed pointed out as a potential avenue with less issues, but if I recall didn't really fix it completely. If you're running wired+iSCSI you're probably much less prone to this. Try and yank some network cables during backup and see how it handles it.

I ran into more issues than most because the particular AP I have at home doesn't work well with the macbook air I was trying to backup and resulted in a lot of disconnects. So it was a bit of a stress test but the issue is real and well documented. You can find instructions all over the web on how to fsck sparsebundles to try and get back your backups[1].

This is particularly annoying because Time Machine is supposed to be a user friendly version of versioned backups like you can do with rsync+hardlinks. I have a script to do that for me on my personal linux machine and would love to be able to deploy TimeMachine+AFP for the rest of the family. Unfortunately apple decided it really needed to have hard-linked directories for just this case and so decided that the way to do that over the network was to have a single binary blob with a HFS image on the server instead of the proper files in the filesystem (filesystems don't usually support hard linked directories, HFS was hacked to do it). That way you not only lose direct access to the individual files on the server you also lose the whole backups when there's disk corruption...

I should probably have a look again to see if iSCSI is a viable solution to this.

[1] http://www.garth.org/archives/2011,08,27,169,fix-time-machin...