If they look and can't see anything then ask what else could be causing the pain. Something is bothering her so go to the Dr and make sure when you leave with a course of action for SOMETHING whether it is ears or something else. No need to feel scared, there are lots of things that are harmless that could cause discomfort, like a tooth issue, swelling of the glands near her ears related to fighting to perpetual cold, sinuses, a muscle that got strained or slept on funny or hit etc.
But ear infections seem to be really often missed by GPs (going by my friends experiences, we've never had an ear issue) and if you do discover an ear infection that was missed by the first GP.....well you certainly wouldn't be the first to be in that boat, it seems to happen a lot.