I built a Trapper early in the summer. Originally I thought I had some holes that were off also. Fully assemble the gun according to the instructions before you start work on it. Make note of any holes that won't line up. Some of them that look wrong, might turn out right. Most of mine did.
I had trouble with the tang screw hole looking like the wrong angle also. If I remember right, the instructions mention attaching it to the trigger group before attempting to seat the trigger group in the stock. That worked for me and I didn't need to alter the hole. They also mentioned that the hole might need adjustment though. If it does, it's easy to grind it out a little.
It's not uncommon for kits to have holes that aren't aligned. It's a simple fix. Take wood glue and glue toothpicks in those holes to fill them. Let them dry, then cut flush with the wood. Reassemble the parts again and mark the new holes, then drill. Only takes a few minutes to get everything all aligned.
The Trapper was a pleasant kit to build overall. I wish you the best of luck with yours, and if I can be any help, just let me know.