Seeing as I'm new around here I'll post a few things that i've never quite understood (maybe not strictly fm2012, been playing since Champ Man > fm2005)
Offering a contract to a free agent who then goes on to ask for double what you can offer. Then seeing him go to a similar club on the decline for half the wages he was asking for with less bonuses! Same happens with transfer fees, regardless of being in the same/different league, same reputation or whatever. You'll offer a fair deal, get rejected, another A.I club offers less and the transfer is accepted.
Also giving team meetings, telling the team they've done well and will stay up...a player disagrees and the whole morale of my team is abysmal. Grrrrreat.
Match engine wise the biggest thing is A.I comebacks, sure once or twice a season is fine but my first season in the prem as Charlton I think the A.I came back in 8 or so games, literally I couldn't hold a 2 or 3 goal lead - even if I was leading by the 75 min mark. My fault? Sure, I could take a striker off, bring on a DMC/DC, waste time, play defensive...still the A.I come back. Keep things the same...A.I come back. Go for broke and attack...A.I come back. Using 3 different set ups my team were comfortable in.
We've all been there...those games you KNOW you'll lose. A player with a long shot stat <10 drilling a 30 yard shot in, or one with a FK stat of 10 curling a ball up and over your wall into the top corner. Or a 5'5 winger with a heading and jumping stat under 5 beating your central defenders to head a ball so fast your keeper just stands there. Or your goalkeeper fumbling a easy shot and so on.
Also being forced to play a younger/back up player and every single goal the A.I exploit him somehow, yet the A.I can use a under 18/backup player who plays better than their first option! In one game I had to use Barzagli who I brang in as cover v Stoke. Stoke. Peter Crouch. Yup he bagged a hat trick cuz Barzagli had a heading stat of 8! Shocking.
Injuries/Red cards. I swear to god as soon as one of my players finds a bit of form or if I'm short in one position that player will get injured! It's like once every 3 games somebody is getting a 2+ week injury. I actually played a key game where I lost 2 players to injury in the opening 7 minutes, made a sub at the 60 min mark and lost another player! Or if I'm leading a game comfortably one of my players decides he wants to miss then next few games so two foots a player in injury time getting suspended for a hard run of games (I'm looking at you Gago!!)