I have experienced this with Trick Flow heads before. It is likely not the head's fault. To have room to CNC the ports as large and straight as possible, Trick Flow machines the bolt holes on the small side, but plenty large enough for the fastener. The problem is that the factory bolt holes in the block weren't the most accurate, but the extra room in the factory head bolt holes allowed the heads to fit just fine anyway. Also, the factory bolts have a somewhat smaller shank diameter than a stud, so that gives even more clearance.
You can open the holes slightly, but be careful you don't break through into the intake port. I would put the gasket on the deck and take a close look at the bolt hole locations in the block. It should be obvious if there are holes that are shifted.