If you mean kind of like 'rabbit ears' at the beginning and end of your grafting one way to get rid of it is to slip the outermost stitches at both ends of both needles over the stitch next to it. This also means 2 less stitches on each needle to graft.
If the 'bumpies' are from uneven tension, try sliding a darning egg or other small round (unbreakable) object inside the sock so you can see the stitches form as you graft and adjust your tension as you go. I sometimes find it hard to adjust all the stitches at the end, especially with very thin yarns.
If it's something else then I'm :shrug: :?? clueless and would like to hear other ideas too.
I'm one of those crazy people who LOVE Kitchner stitch. If you want to get REALLY good at grafting take a look at EZ's mystery blanket sometime - squares started in the middle on 4 stitches, knit outward, then grafted on all sides to the squares adjacent, outer edges put on really loonnnngggggg needle (I had to hook all my Denise's together) and the edging knitted outward with mitered corners.
The mystery is it's really hard to tell where you cast on and bound off. Fun!