A bicycle is a simple machine but the devil is in the details. If you think about it logically, the shifter pulls a measured amount of cable and that cable pulls the derailleur a set amount. Assuming you have matching parts: the cable tension can be wrong, the shift cable is binding up, or the derailleur and cassette are somehow not aligning.

If it ever worked right you can assume the parts match. Limit screws don't move on their own so you can exclude them. Most guys by the time they get to your point can identify sticky cables and will fiddle with cable tension till they get frustrated. That leaves derailleur hanger alignment. If you have a 9-speed or 10-speed cassette it doesn't have to be very far off to screw up your shifting.