It's been on my Annoys Me list for months now, and it seems to happen regularly, while not pervasive it's there, in the COL and HS leagues for me; occasionally a minor league team. Something in the load game logic makes it think the logos or uniforms are in need of updating or 'assignment' I think it calls it during the load. Now I don't worry about it much; just change it when I see a wrong uniform in a pic. Honestly, can't remember a logo changing, it's been uniforms in this world.
Not a game-breaker, just a little irritating.