MoF stage 4 near the start can generally be prevented by starting from stage 3 (fast-forwarding is fine).
SA stage 6 Utsuho's first nonspell can generally be prevented by starting from the beginning (stage 5 may work, but if it doesn't, stage 4 probably won't work either but beginning should work, in my experience)... annoying, yes, but at least it's watchable.
PCB desync, if it occurs, will not be preventable as far as I know. At least it's much rarer than those two. It happened to me once, but this is the second time I've ever heard of it occurring.
It's never occurred in any other games for me.
Sometimes I wonder if in MoF+ it relates to potential variance in stage loading time, that might be prevented by always remaining still during stage transitions. Just a theory without any evidence though (just like the theory that not shooting when Shinki appears prevents the random death glitch, which turned out to be untrue).