I wouldn't worry about it too much... it's much more likely that they are backed up at the moment like they say they are, rather than cooking up some elaborate plot to defraud the instructors they depend upon. If withheld taxes were being systematically inflated in this manner I'm pretty sure people would be screaming about it on this forum, and they're not.
I just don't see them doing anything underhanded like that. I wouldn't panic unless you actually see your tax withholding increase. Given that you submitted the documents when required you should be OK.
