The MD/PhD Trap
Caveat: The MD/PhD trap section is merely a guideline/thought process and should not be taken as gospel.
Academic programs in competitive specialties often have Step I cutoff scores for interview. Even if not a strict cutoff, step I scores, clinical grades, and LORs are examined closely. These factors are almost always far more important to programs than the research you have done. Thus even with a merely average medical school performance, you may not get the specialty you want.
It goes without saying that many programs will automatically cut students who have serious academic issues ranging from failing a course to failing a year to a bad LOR. I am not talking about these students with serious "red flags". What I mean is that to match to strong academic programs, you need to be a strong medical student in addition to having a solid PhD.
So MD/PhDs need to be strong medical students to match to competitive academic residency programs that have the research opportunities we need to persue academic careers. Conversely, MD/PhDs are essentially excluded from categorical community programs. These are the programs that usually match MD-only students with lower step scores and grades than the average for a specialty. These are your standard "backup" programs. But these programs know they don't have research to offer and assume an MD/PhD is going to go elsewhere. Even if an MD/PhD student tries to spin otherwise by downplaying their research experience, they will likely not be interviewed or match there. I've heard some stories of antagonistic interviewers along these lines--"What are you doing here? We don't have research!"--"Where else did you apply? You'd never come here." I've seen several applicants get burned either by thinking community would be a backup, or by applying to mostly community programs in some specific geographic region for family/relationship reasons.
Thus it is possible to be caught in the middle. If you have a merely average medical school performance, you will often be shut out of research heavy academic training programs for lack of competitive statistics such as step scores and AOA. Yet if you are an MD/PhD, the community programs don't want you. This is the trap which can lead to you not matching. If one wasn't so research-heavy there would be a chance to match community where your MD-only classmate with similar stats matched. But you can't match at those community programs. In these situations lower-tier academic is the best bet, but still risky.