Why are my Shimano 105 11-speed shifter/derailleur acting like they're 10-speed?
It's evident from your first picture that there is definitely a pretty bad derailleur cage alignment issue. 

The derailleur hanger does not appear bent, but it does look like the derailleur bolt may be cross threaded , as the derailleur body seems to be at an angle to the hanger.

Check the derailleur installation and also check that the cage is not bent.