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For stress testing purposes, I have OmniFocus doing a sync every 30 seconds, and I have a very large database with lots of files most of the time, in a continual state of flux. I also have Time Machine running. I have yet to have any sort of hang, except when a disk starts going bad. I think if there is a general problem with OmniFocus coexisting with Time Machine, we would have heard about it by now!

Quit OmniFocus and have Time Machine try the backup again. I suggest this not because I think there is some interaction, but because I want you to have a complete backup in case there is a failure of your disk happening.