Like death and taxes, pulled threads are inevitable and should be dealt with quickly and proficiently. This is especially important on woolens such as flannel. I had a pulled thread on a Brioni suit and was rather ignorant of the best way to proceed. Whatever you do, DO NOT cut the pulled thread loop. That could be the beginning of the end of the suit or garment in question.
Here's the link to the StyleForum thread I created on this issue. There are a few ways to deal with this. Basically, you'll need to thread another needle through the offending loop and "pull" it through to the underside of the fabric. Good luck!