Wood filler or leave as is. Maybe even use a bit of tite bond as the filler as it should dry a light colour if not clear.

Most of these kits with set necks all have joints that are hard to get right. On the only one that I built with a set neck I was paranoid about the glue spewing out everywhere but in hindsight that could have been better as it would have completely filled up all the gap joints that you can wipe away whilst still wet or lightly sand once dry and cured a bit more.