All of my A fares show up in my account as:
Class Paid/Flown : Q/A (or whatever the fare basis is, maybe K/A or H/A etc)

I also have a line showing:
Delta 50% Class of Service Bonus for UP fares

If you selected first on the website, then you should get the bonus miles and MQM for the A fare. There is no such thing as an actual 'A' fare basis... they are all comprised of some sort of UP basis. Same with P, except those are usually the fare basis with a WNUP designator attached on, which occurs when there is either no inventory left in the A bucket and/or no -UP fares that would book into A. Note that I've seen a fare on one or two occasions where it doesn't explicitly have UP in the fare since they run out of room for characters and just has a U in the middle instead.

Was one of your legs on an RJ with no first class? That could help confuse the system. Other thing is that U fare basis could be some special that was being run that the awesome IT system couldn't handle correctly.