I'd check the squareness of the neck heel, then check the coners of the neck pocket for burrs or little remanants from the routing.
Sometimes there can be a little step in the corners that props up the neck to leave gaps like that.
You may also just want to check that the fllor of the neck pocket is even and level and that the radioused corners of the heel and the pocket fit properly, particularly in the very bottom of the pocket Radii.