I honestly can't see a problem. Those two little holes are probably about 1mm across? and they are on the seam where the material is sewn together.
Unless you pose your figures with their legs spread so you can continually stare at their crotches, I can't see why this is even an issue.
It's probably getting worse every time you open his legs to take another photo.
Seriously, just be grateful for what you have got.
How about I just send it back, and get a new body that isnt fused and doesnt have holes in it?