I don't think any military surgery program is notorious, with the possible exception of the AF residency at Keesler, where they matched residents into a program that failed its RRC site visit and is not accredited.
But all are severely challenged by the dowsizing of military medical centers. Case load and acuity are big, big problems. I only have personal experience with four military and two civilian training programs, but based on hearsay, it would seem that all are having issues. The AF has folded two of its programs into nearby civilian facilities and no longer has any accredited free-standing programs. The Army and Navy programs are still trying to make a go of it by doing a lot of outside civilian rotations.
If I had to guess, I would say that the combined Wilford Hall/BAMC surgery program may end up being the best in the military. The combined institution may actually have enough cases to train the four residents per year that are planned. they also do level I trauma and have a burn unit, so that may bring in some high-acuity cases.