Well, my first thoughts are (since you posted in another thread that your horse does great barefoot) that the hopping and fighting the trimmer is to blame. She likely has a REASON for the fighting. She might be trying to tell you that your farrier holds her leg up at a weird, uncomfortable height that's convenient for him, but not for her. How old is she? She may have a touch of arthritis in her hocks or hips and the trimming is aggrevating it. Or even if she's just short and your farrier is a big guy, that can cause some problems.
She could have strained or pulled a muscle in the fighting. Some horses have more trouble standing on three legs thanks to being fat or poor confromation overall and balance is hard to maintain.
How is she to have her feet picked up when it's not the farrier? Does she start out okay with him and start to struggle after he's had it up for a while? Maybe she just needs to be able to put it down periodically. If she's a dink all the time about her feet, it's probably a training issue. If she is normally good and just starts to struggle as your farrier works, I would say it's more of an issue of how he cradles her hoof or how far he cranks her leg away from her body, esp if she has any underlying stiffness.
And, of course, she could have brusied a foot on a rock, but if she's normally tough footed on them, I'd say it's not that, but soreness in other parts of her leg (like the hock or stifle). And bruises don't usually show up as sore immediately (usual being the key word).
Me, I try to understand and will squat lower for short, fat or older horses and give them breaks. Young, athletic horses that still fuss after a few minutes, I start to think they have sore hocks or stifles or even in the back, esp if it's consistent on the same leg and when I hold it a certain way.