If you have been using the crate since she is a pup she might be happy with it. Most pups tend to view their crate as their safe haven, it's where they go to rest and is not a bad place. Personally I think it's great that she likes her crate. Maybe she is tired and just not ready to get out. I leave Raven's crate open and she will go in and out. She will get out when she is good and ready. I have always tried to make it a fun and inviting place for her so she doesn't see it as something negative.
If she never peed on the way down to go out before or done it since, I would just watch it and chalk it up to an accident.