The Compare function has an optional step that allows for manaully adjusting the result.  Ideally this should not be necessary to use.  First try adjusting the compare tolerance.  With a larger tolerance, the very fine differences in the parts will be ignored.  But if you need to use the optional step for manual interaction, here is what the help says about selecting certain faces:

  • To complete the "pick" operation, press  (middle mouse button) after selecting the face(s).
  • If an Unchanged Face is picked, it turns to red (old face) and it will be removed.
  • If an Old Face or Old Coincident Face is picked, it turns gray(unchanged) and it will not be removed.
  • If a New Face or New Coincident Face is picked, it is hidden and will not be added.

To summarize, red and gray faces switch back and forth between these 2 designations.  Blue faces are simply disregarded and can no longer be viewed.  It's best to use the display legend and only work on one grouping at a time so you can keep the selections clear.