This may have not been the issue, but sometimes, if the lugs are not marked correctly (front to back AND in order), you can take out the barrel to fix or finish the stock, and if you are finishing the barrel (Draw filing or bluing) you take off the barrel lugs. Now, like this has never happened to me, if you put the "wrong" order of lugs back, I bet those little holes will not line up like they did during construction. Having the pins in and out during building normally opens up the wood enough for a pretty easy slide through the stock, when running into a "hammer fit" on any drilled lug, thimble or guard, If I felt any resistance, I would stop before I could do damage.
I have a 6" piece of 1/8 Piano wire that is tapered on one end, and polished bright that I use to "Hole check" any pin hole before tapping in the final pin.
Just a thought, those pesky lugs and such can get out or order pretty quick.. Mark them with a file, not just a sharpie, as that can wear off..
Jon