I've encountered the exact same problem. Players keep playing for their previous teams. I'm managing Gainare Tottori and I have two players that are contracted to my team, but still play for another team and show up in their squad list (Hayato Nukui and Masaki Kaneura). I also have four players that are contracted to other teams, but still show up in my squad and tactics pages (Koki Ishii, Kosuke Masutani, Masaki Kaneura and Kentaro Shigematsu). I think it has something to do with using "Real World" when setting up the game, because at the start of 24.3 database all these players are at their previous teams.