I think most often it's because of board pass rates, which is why programs weight Step scores so heavily during the application process: USMLE scores are correlated with board scores, and if you're a bad test-taker then a school may risk its accreditation by accepting you into their program (as explained to me by one of my mentors; most programs just want to be sure you will pass your boards).
That means smaller programs are more vulnerable to probation: if you only have two chief residents, and one fails their first attempt, the program's pass rate for that year drops to 50%. (Also see:
http://askskepticalscalpel.blogspot.com/2014/08/board-passage-rates-and-residency.html)
I know that Robert Packer/Guthrie is on probation due to low board pass rates (I was told this by the program director, who also commented on their revamped curriculum to help prepare students for success on the boards).
Work hour violations can also lead to probation, and I think if residents complain about supervision/quality of training/cultural climate of a program, that can lead to probation as well.
In general, from speaking with PDs, I've noticed that programs that are or have recently been on probation seem highly motivated to make positive changes, so that can be a real benefit to new residents. If a program has a specific and detailed plan of action (totally appropriate to ask about this in interviews), that would be very reassuring.