The tubing on which the spare tire sits, combined with the very tight fit against the bottom of the TM, will often create two parallel "impressions" of the type which you seem to be describing.
If that was the cause, then you might look at two fixes. Fix #1 rests the spare tire on two plates, instead of the two thin bars. Here:
http://www.trailmanorowners.com/foru...ead.php?t=5672
And Fix #2, lowering the spare tire carrier down by a bit less than 1" (so that it isn't squeezed so hard between the hanger and the bottom of the TM body), is discussed at the end of that thread in my version, but also has two other variations (by Eric and Bill) shown WITH PICTURES in this Thread:
http://www.trailmanorowners.com/foru...ead.php?t=5828
If you do fix #1, then fix #2 is mandatory-- the added thickness of the plates makes lengthening of the carrier "hanger" distance even more necessary.