Here are a few limitations and caveats to be aware of.

Some games are designed to only accept “raw” input, i.e. input from physical devices. These games will not detect key presses or clicks generated by Alt Controller.

Alt Controller usually cannot draw screen region or mouse indicator overlays on top of games when they are running in full screen mode. However, some games have an option to run inside a window, which may allow the overlays to be visible.

Alt Controller may not be able to detect key presses that were generated using some onscreen keyboards.

Certain Windows scaling (DPI) settings can cause Alt Controller to interpret screen coordinates incorrectly. A helpful user has reported this solution to the problem: right-click the Alt Controller shortcut, choose Properties (Compatibility tab), click “Change High DPI settings” then tick “Override high DPI scaling performed by” and select “System”. Click OK twice to apply the changes.