Not concerning if the pickup pole pieces line up where they should be (need a perfectly frontal shot for that), but a bit unexpected and not ideal. I thought they'd use templates or the CNC for drilling those.
I wouldn't try filling the holes and re-drilling as that tends to have mixed resultswhen they are too close to the original ones. Even with a drill press a small drill bit will shift/bend ever so slightly to follow the path of least resistance, which is unfortunately almost always the hole you just plugged.
If it doesn't bother you then cool, my OCD would be bothered a bit ;-)