I'd imagine that if it didn't fit right (too long for the horse's back or the seat was too small for the rider, causing the rider to sit against the cantle), then I'm sure it might cause some issues.
Also, treeless saddles MUST be used with appropriate pads. You cannot use a "normal" pad with most treeless saddles. So you have to take that in to consideration.
Endurance riders have logged tens of THOUSANDS of miles in treeless saddles in the USA, Canada, Europe, and Australia. These rides are heavily monitored and the horses vetted at frequent stops on the ride. If the horse shows back soreness, the rider is pulled and is not allowed to finish the ride. Do you think these riders would take a chance at using a saddle that would sore their horse and get them pulled from the ride? I seriously doubt it. In fact, the 2007 winner of the prestigious Tevis Cup 100 mile endurance race won riding on a Freeform Treeless saddle and I believe a Haf pad (the brand is Haf, from Germany).
So, yes, I'm sure a treeless saddle COULD cause problems, if it were wrong for horse or rider, or not used with the right pads, but no, I don't think they inherently cause problems. I have a Bob Marshall and Skito pad too. I am a heavy rider (250 lbs) and have never had any problems with my horses in the 2 years I've been using it so far. I know endurance and trail riders that have logged thousands of miles in their Bob Marshalls with no problems either. There is a reason quality treeless saddles hold their resale values so well