really screwed up their interview or have a notable deficiency in their application?
There are too many unknowns here (identity of the program and its post-interview stats, your interview performance, whether the PD had their coffee that morning etc) to make any insightful comment about whether or not this is the case. Assuming your numbers are competitive for the programs you applied to and you already have a decent number of IIs, I wouldn't fret about your paper application. If you thought you did well on your interview, then you probably did, although there's always room for improvement in the future.
I was rejected from MSTP with MD-only waitlist from the program where I felt I interviewed best. I think they felt I wasn't a good fit for the institution, based on a variety of different factors including location and research interest alignment. Something similar could have happened in your case. Don't lose sleep over what could have been, especially when you don't know why.
What likely happened is: you didn't make the cut for MSTP (for whatever reason), so your application was forwarded to the MD committee, who had either concurrently reviewed it or quickly reviewed it after receiving it, then determined they had already filled their quota of X number of MD seats by December, and consequently put you on the wait-list. At most institutions, MD-only applicants get first dibs at MD-only seats.
I have slightly below average (for MSTP at least) clinical experience, so maybe that's what held me back?
If you received an II then this is unlikely, unless you were asked a bunch of questions about your clinical experiences (also unlikely) and you bombed those.
