Audio and video gaps, what do they mean and how to fix them?

When I demux with "UsEac3to" some .mkv files I find things like that (there are many more lines but I show you only 5): [v01] Video has a gap of 1 frames at playtime 0:06:12. <WARNING> [v01] Video has a gap of 1 frames at playtime 0:06:15. <WARNING> [v01] Video has a gap of 1 frames at playtime 0:06:18. <WARNING> [v01] Video has a gap of 1 frames at playtime 0:06:21. <WARNING> [v01] Video has a gap of 1 frames at playtime 0:06:24. <WARNING> The same with audio. What kind of problem or error do these files have? Is there a way to fix them or are the resulting audio (.ac3) and video (.h264) files already fixed after demuxing?

Apparently, even the author doesn't know the answer: [v01] The video bitstream framerate field doesn't seem to match the timestamps. <WARNING> Demuxing these tracks may still produce correct results - or not. <WARNING> Could it be due to pulldown?

I don't know if is the pulldown, sometimes are TV captures with lost frames. Like madshi say the extracted tracks can preserve the sync or not. If not you need extract the timestamps and apply them to the final mkv.

Yes, my rips, ripped from the original Blu-rays. I don't have much experience but I always use "Handbrake". I always select, for instance, Framerate (Same as source), Constant Bitrate, x264 Tune (Film), H.264 Profile (High) and H.264 Level (4.1). I decided to demux some rips with "Useac3to" to test them and I’ve found audio gaps, video gaps, audio overlaps, video overlaps… and I don't know what I've done wrong.

As a comparison, I suggest you give MakeMKV a try and encode directly to .mkv...