What does the model look like shaded?
I'm guessing from the pictures that there is solid geometry that is the inverse of the hole and pilot, but that doesn't make entire sense. Still, that's what it looks like.
One way to tweak this sort of situation is to use an orientation plane that is not at 90 degrees to existing geometry for linear protrusions or sketch planes not perpendicular to the sides for revolves. This avoids having some geometry almost aligned, but not close enough to be actually aligned, causing the software to fail.
I don't know how an orientation change can be applied to holes, but if it works for cuts then that's a start.
The other try is to insert the failing hole ahead of all the other holes to see what happens.