I was playing a team game and I had to attack my teammate for a bonus. But, I accidentally clicked something so it now doesn't bring up the option to attack or transfer a teammate. It automatically transfers unless I check "Treat Teammates as Enemies" for every single move.

You checked the "Don't ask me again" box, so it's not asking you anymore. You can change it back on the Settings tab.

or you can use the "advanced" button when making an attack order.