I actually ran into this issue a few times working on my reconstruction of Godzilla 1985; sometimes a shot in the copy of the (edited) US version I was recreating would go on a frame longer or begin a frame earlier than the same shot in the HD copy of the Japanese version I was using to upgrade it to HD.

(There’s also the fact that the US Blu-ray of the Japanese version uses the Japanese HDTV master as opposed to the master used for the Japanese Blu-ray, meaning that there are some missing frames around reel changes.)