Is my rear shifter broken? Ultegra 6800 shifter, 11 speeds, 9 clicks, only 8 causing cable tension change
You’ve taken the derailleur out of the system and still see the problem, next thing I would do is replace the cable. They have a bad habit of getting chewed up by the shifter and misbehaving, but you can’t see the damage. Very rusty cables give issues too but you’re unlikely to have a low quality cable, and would be able to see the poor condition. 

Give it a try and update the question if there’s no improvement... which would only leave the shifter as a culprit.