Recently started playing bass, and am constantly missing the F and F# notes. Even when I reach over with my thumb and press as 'perfect' as possible. Is this common?

Make sure you crank your volumes all the way up on your bass and calibrate it within Rocksmith.  Helps a little but i've found there's not a whole lot you can do, Rocksmith just doesn't do well on some of the bass tones.  I've got a bunch of downtuned deftones songs etc. that I can't ever break 70 or 80% on because it just doesn't recognize the notes even though I'm hitting them.  

Hmmm, A few questions, but few answers

 

Are you fretting too hard and pulling the notes sharp?

 

Are you accidentally bending the string sharp?

 

Is you bass properly intonated? EDIT-proper set-up? including neck relief, string height, nut height, saddle height, etc.

 

If you go into Riff Repeater, there is a live tuner in the bottom left corner.  You could play the F and F# and look at the reading to see if you are sharp or flat and then adjust your tuning to the "least worst" compromise