WWBL,
That has happened to me as well. When trades process, sometimes players end up on the correct team, sometimes some in the deal will stay on their old team.... some players just magically appear in the free agent pool.
I state again, when these things happened to me.... I imported lineups FIRST. Because... that would just make too much sense
Also, when I did have these things happening... it was in an online league setting, where there was a mix of human and AI teams... and trades that were messed up like this was when a human team finished a good deal with the AI.