restarted the save keeping track of what coins I picked up where, and the coin I was missing was one that I did find on my first attempt. at least the bug does not seem to be very reproducible, so its probably not a big deal, as even if it does happen again, replaying from the beginning to fix it isn't nearly as time consuming as the first attempt.
Thanks for your feedback on this. I'll do a little investigating and see if I can figure out what might cause a bug like this. Sorry that it impacted your first play through! And yeah, you can definitely do things a lot faster the 2nd time around. Personally I can do a full run through in about 10~ minutes!