There are incantations that can dump for you metadata about the individual packets a given video stream is made up of, ordered by timecode. That way you can sanity check things.
This is terribly frustrating. The paths of least resistance either lead to improper cuts or wasteful re-encoding. Re-encoding just until the nearest keyframe I'm sure is also possible, but yeah, this does suck, and the tool above doesn't seem to make this any more accessible either according to the sibling comment.