control with controller

I've noticed similar issues - only ever seems to be with the trigger (R1/R2) buttons, although I haven't specifically noticed it during a button mash - I have noticed it during some passages of play where I need to use a force power for example, or trigger Bode to do something - it either flat out refuses to trigger the action (usually Bode trigger) or activates the action, but the game ignores it (usually when trying to force push/pull something).  If I switch back briefly to using keyboard and mouse - it works fine- then I can go back to controller.

As for using only one of keyboard and mouse or controller - it's a PC, most folks use it for more than just playing Jedi Survivor so I wouldn't say that's a reasonable workaround.  I've yet to encounter it causing me a major issue as it tends to be in railroaded scripted segments that I've noticed it, rather than during combat/open play.