the CA FTB is the only tax agency thus far to ever send me a letter disagreeing with what I had filed. The gist of it was that I had made a multi-decimal-place error on one paycheck when requesting extra withholding, and then left it still too big by an order of magnitude after I tried to correct it (b/c the year before i had owed them ~$4k and I prefer the psychological feeling of getting a small refund) which resulted in getting a refund so large I triggered some automatic "this must be a mistake" audit.

I had slightly complicated taxes that year and actually called them and spoke to someone who helped narrow down the number of forms I needed to dig up and submit to just a single form from one employer, and confirmed that it was due to the above withholding anomaly. I sent that form and a couple months later they sent me a letter indicating that my original number was basically correct. for some reason they preferred a number that was lower by a few dollars and I really didn't care, so I happily cashed the refund check (which was for several $k (IIRC between $5-10k, which i did care about).

The next year I had to file an extra form - apparently FTB had held my refund for long enough that when they sent it back to me they also paid me interest on my refund, and I had to file for taxes on that interest...