Limping (obviously), pinning ears when you touch specific places, moving more stiffly and unwillingly than usual, and a grumpy attitude can all be signs, though of course do not all mean pain all the time. I'm sure others can offer more I missed.
Her back and legs would be the most important I suppose, and really since you know her personality better than anyone, is she acting different than normal? Something off? Besides being tired of course. You can be a better judge than us :)
Don't judge someone's horse or skill because they don't compete or work with a trainer.
Sometimes they're the most in tune with each other.