I think it could happen if you issue a revised LE due to a rate lock, and update the fees at that time, but didn't have a valid changed circumstance. But, maybe I haven't thought this through enough or am missing something. See if this makes sense to you.
EX:
1. Initial LE - appraisal fee is estimated at $250 and it is 0 tolerance
2. Realize you made a mistake and the company you disclosed recently changed their fee to 300 but you forgot to update your template. You don't have a valid changed circumstance.
3. You lock the rate for the borrower and issue a revised LE. Since you know the appraisal cost is actually 300 you update it on the revised LE at that time. However, since you didn't have a valid changed circumstance, you are still over tolerance.
4. When you issue the CD, you use the amounts from the most recent LE which include the 300 for the appraisal. So the most recent LE and the CD match, but you still have a tolerance violation.