I was from Pitt. It's hard to say what the cause is since I have not attended other medical schools. I don't really want to badmouth my alma mater, but people should know.
My hypothesis is that one possible cause might be due to the old fashioned teaching done there. The Pitt ethos is to jam pack your entire day with as much stuff as possible (e.g., with lectures, PBLs, etc) which gives little time to study on your own. The lectures given by faculty are much less high yield and lower quality than what can be found online nowadays, but Pitt faculty had trouble accepting that. They have changed now somewhat, so I have heard. Students don't really learn from in person lectures anymore; it's more online and self study nowadays because the online lectures are so good. Not even sure that med school lectures are needed anymore tbh. The ethos ultimately might cause a low step 1 score despite working hard. Also, Pitt gives 3.5 weeks for Step 1 studying, and they are *very* resistant to giving you any more time. Contrast this to say a place like Yale where the ethos is more self learning.
The Pitt ethos also holds during the clinical years. Days are packed from 7AM until maybe 5PM. The more packed, the better, so they think. Faculty are proud of their dedicated teaching sessions despite the fact that they are subpar and just get in the way of learning for the shelf. Faculty often pimp you on things that frankly do not appear on the shelf exam and are more intern level (e.g., doses in IM, that odd nerve in surgery). It is therefore difficult to get a good shelf score and a good clinical score at the same time. I assume that this probably holds in other schools as well, but maybe not to the extent that it happens at Pitt? Clinical rotation length are also on the shorter side. IM is 2 months, surgery is 1.5 months, Peds 1 month, OB/GYN 1 month, etc which gives little time to study for the shelf exams. Instead, Pitt requires a rotation called specialty care and CAMP-C which take up 3 months in 3rd year which no residency really cares about. Faculty also almost always request patient logs, essays, super detailed H&Ps, etc that are more busy work than learning.
Again, this may also happen at other med schools, but I have not attended them, so I can only say for Pitt