Throttles are usually 5v, running right off the controller. Most controllers can't handle more than 12v input on the thorttle signal line, or on a variable-input braking line, so if the signals from yours are above 5v, they could cause undesired operation (and if the inputs on the controller are not designed correctly, damage them).
Quite a few scooters and motorcycles with tail/brake lights use a 12v converter for those, and use a "high level" brake input on the controller for a brake switch connection, because the same swtich in the lever/etc usually controls the brake light directly...and wiring one like that directly into the "low level" brake input of a controller can damage it as it's only meant for 5v max there. But this isn't a variable input, it's just a switch input.
If the bike doesn't have a complete wiring diagram for every wire on it, I'd recommend looking up the manual for your controller model on siaecosys / mqcon, and verifying which wires in your system go where on the controller, and what voltages are actually present on those inputs. If it turns out there *are* 12v signals on 5v inputs, you'll probably need to rewire the signals to operate from 5v instead.
Whether taht will make the controller operate correctly depends on whether anything was damaged or not, and what settings the controller has both in what you can access in user settings, and what is factory set that you can't even see.