We did have an incision problem with our dog Merlin after he had TPLO surgery for a ruptured ACL.  He seemed really bothered by his incision - sometimes he would wince and jump a little and then look at it like something had pinched him.  Also, one tiny (1 cm) spot in his incision didn't seem to be growing together like the rest, even though he never licked or bothered it.  We finally took him to the vet and here's what we discovered:  With most major surgeries (amputation included!) there is an internal set of stitches and also the external ones that you can see.  Apparently, the surgeon had tied off the internal stitches and left the "ears" of the knot too long.  Since the stitches are very stiff, those "ears" were working back and forth when he moved and basically ripping the incision back open over and over in that one spot.  This led to the exterior incision also not healing.  The vet had to re-open the outer incision a bit, clip the "ears" from the knot on the internal stitches and then sew up the outer incision in that spot.  That seemed to do the trick.

Not sure if that is what is happening with your kiddo, but worth keeping an eye on!  Good luck!