This could be a “hands-on” thing, where you need to be touching the horse.
Start with checking the tack, saddle for a stitch knot, uneven padding, thin padding in that area. What kind of pad? I hate thin ones, horse feels everything. Pad might also have a worn spot, thin place in the depth of his cushioning, allowing horse to get 'bruised" when ridden.
Have boarder tack up as usual, then get on horse. You try running your hands under the saddle where she is sitting, then under the pad on horse skin. Can you FEEL any extra pressure on the spot that gets the bump? Sometimes weight in the saddle changes how things fit on horse. Then watch her ride, she may be riding unevenly or coming down harder at certain times, so is impacting that spot harder than the rest of his body.
If you can’t find anything, having a saddle fitter check things could find issues you missed with less skilled training.
We had a saddle “go bad” on us after using it for quite a while on one horse. Horse was NOT happy, when he always had been before. Took horse and saddle to the Saddle Fitter, who told us after checking saddle that the tree was warped! One part was just digging into horse, so he was TELLING us he had a problem.
Thinking back, saddle got used and soaked during an incredibly heavy rain storm. It was High School Equestrian Team District Meet, could not avoid riding. There was over 12 inches of rain, with kids competing in it!!
I had let the saddle air-dry over a week, never thought about possible tree warping that the Saddle Fitter found. Had to get the kid a new saddle, since she needed to ride daily and couldn’t get the other saddle a new tree in time to keep things rolling along.
So always surprises to be found with saddles! Try helping her with the hand testing under rider. If nothing is found, time to get a Saddle Fitter involved. Her tack might just be wrong for the horse or there may be hidden issues. Either way, horse getting bruised and sored each ride, is going to make him CRABBY. He will quit cooperating since it ALWAYS hurts to be ridden. Things could get ugly.