Your part has a number of issues, the most serious being hole sizes. The part has these (in the gerber):
INCH
T100C0.082677
T101C0.043307
The first being the two mounting holes and the second being the
5 pin holes. Neither seem to be standard drill sizes, the first will probably round up to .0860 and the second to .0520 (being slightly larger than the standard .042 used on the 1n4001 diode for instance). They are also quite different from those in the enc_Baseline.fzz file which are:
M48
INCH
T1C0.125000
T100C0.039370
T101C0.038000
Which are 1/4 inch for the mounting holes and .038 ( the standard hole size for .1 square posts) for three of the pin holes and .039 (which I expect should be .038 like the first three) for the two switch positions. As well since schematic (and possibly breadboard too, I didn’t check it) has pins assigned incorrectly you are getting the red square indicating pins not assigned in pcb view in Fritzing. If you can confirm which set of hole sizes is correct I can substitute your pcb view (from either the fzz file or the fzpz file) in to pcb view on my part to get one with a tested footprint.
Peter