Not sure if this is still being looked into but it's happened again but without a red card.
I was taking off a CM for another CM, but wanted to swap the two remaining CM's over. So I used the make a sub option for the swap and the oncoming CM came on, but both of the other CM's came off.
Would you like the screenshot and game save file?
Juve Stabia v Paris Saint-Germain.pkm