If you want to level up a troop with the Medals and but press Square PS 4/5 to take it out then you get into the Skills Menu. You have to go out completely and then back in. I think it shouldn’t be like that and it wasn’t like that before the new Menu was there.
Equivalent buttons for other platforms are Y (switch) and X (PC/XBox).
Can confirm this is a bug: The button prompt shown to deselect/remove a Medal is the same button used to toggle the Skills tab on/off:
You can still deselect a Medal, at least – just cursor over to the righthand side to select the medal in question, then press your Confirm button to remove it.