I've had this go both ways: PTO checks that were deposited by the school, and school checks that were deposited by the PTO. Sometimes, I've written a check to the school when I got the wrong check (class dues go to the school, PTO dues go to the PTO, so you can imagine there's potential for confusion). It's a bit of a pain to get a check from the school, so if it was just $30 dues, we probably let it go. I know in some similar cases, the principal has asked us how we want the money spent and done that, rather than trying to reimburse us.
I think if you go in with an attitude of "I think this was a simple mistake, but the PTO volunteers put in a lot of work for it, how can we fix it?" you'll probably be OK.

So technically we are a PTA at my school, I hope this is ok to ask here.

Im the secretary for my Elementary schools PTA, and we do 2 sprit nights a year at a local restaurant. We did one in November, and the company says it can take up to 6 weeks to get a check, and if after 6 weeks you don't have one to contact them. The check was supposed to be made out to " ______ Elementary PTA C/O our PTA President" and they would mail it to the school. 6 weeks out would have been around our schools Christmas break and by the second week of January we still hadn't heard anything. I emailed the school secretary to ask if she had seen a check for the PTA come in before I contacted the restaurant. She replied saying it came at the end of November and she forget to tell us, sorry. So I told the PTA president that the school secretary said it already came to the school. The PTA president asked her about it, and she said the check was deposited into the schools account and that she already emailed me about it. Even though she never mentioned that they deposited our check, just that it was delivered to the school. This feels like a big " no-no" to me. The check should have been made out to the PTA. My president is dumbfounded and she just said ok and left the office thinking maybe she had emailed me more information, even though she hasn't. My PTA President is not in the PTA at the end of the school year (4 more months) she will be taking a job as an AID at the school next year and she doesn't want to go on a bad note and make things awkward with the principal and school secretary. I don't really know what to do, she asked me not to talk to the local PTA council until she had a chance to talk to the Principal.

Anyways, am I crazy for thinking the school messed up big time? Im not sure what to do and feel stuck in the middle