If your mouse or keyboard input is blocked while in-game, particularly after hitting your hotkey to change overlay settings (default ctrl+o) this could be caused by a conflict with your hotkey or with a 3rd party overlay. To resolve any hotkey conflicts, go to Settings -> Overlay and then change the hotkey.
If changing your hotkey did not resolve your issue, we recommend disabling any 3rd party overlays as they may be potentially conflicting with CAM. Known overlays that have issues are Uplay and Origin overlays. Now in the event that you want to make use of these overlays and do not want to use CAM at all for an overlay, you can disable the CAM overlay outright. This can be done by going to Settings -> General and then you would disable Game Hooking.
If you have any questions or still have problems with losing input in your game when CAM is running, please contact our Customer Service Team for assistance.