I start with a blank lineup then drag all the players in before setting the positions.
I'm doing a replay with real-life lineups and transactions so I know I'm not inserting players that are already in the lineups as I'm referencing the lineups that were actually used by the teams. It also happens when I only have a couple players in the lineup.
I took a video with my phone. The error happened 4 times during the video so it should provide a good example. I'll post when I can upload.
Here you go:
https://www.youtube.com/watch?v=YMHNWlFuwOk