There are holes that aren’t in the right context for the parts they are supposed to be in.
In order to drill the holes in the part where they are located, the hole geometry needs to be in the same context as the part they’ll be in.
You’ve got a hole started in the other part but you pushed it through, too far. See the lower left corner of my screen shots. Some of the holes don’t go through all the way, either.
Do you really want both of the parts glued together as you’ve got them? If I was drawing this thing, I’d make each part I’d make in the shop as a separate component. I’m thinking either you’ve skipped a few important steps in the tutorial or Mr. Bishop left them out.