It happens occasionally, especially with the National Teams and registering players to those. I think it just happens once you edit quite a bit of data.
For me, what seems to work quite well is to not register the players too quickly.
What I mean by this is move to the player you want to replace, then wait, until their body and face is loaded and appears on the right.
Then when you move on to the list of players to swap, wait until the face/body of the first player is loaded and appears on the right. Then find the player you want to put into the National Team, and again wait until the player's face/body is loaded and appears on the right.
Doing it this way, I haven't had any problems. Previously I had massive problems, especially with Serbia and I think Slovakia, whenever I tried to swap anyone from the NT, the game crashed/froze.