1. when starting a hotseat game (lets say with 5 players) at the beginning it says "Player 1's turn" and you click ok and select a color for player 1. then it asks for player 2 turn. you click ok and.. player 2 overtakes player 1 color, player 1 transforms into spectator and nothing is asked anymore. all other stay spectator, too. when you manually click on the players 1 by 1 agai, you can give them colors then.
EDIT: it seems like if you newly started TTS and then open hotseat, it works properly. but go back to main menu and open hotseat agian, then it will be bugged

2. then after you did all that, and you load another mod, the colors change of course since each mod can use another color setup. so you need to re-assign the colors anew to the players. so re-assigning colors to hotseat players after loading another mod causes this: you move an object, then automatically the select box is triggered (which is usually triggered if you dont click on an object but on an empty space and hold down left mouse button. that ay you can select multiple items. thats what i mean with "select tool is triggered" )
so yeah, after you did the first step described above and switch to step 2 (loading a new mod and re-assign new colors), moving objects causes triggering select tool automatically while moving objects. and of you click at stacked objects, 2 at once are picked and moved, never only 1.