Be sure to update to the latest version of eac3to. There was a bug in that version extracting HEVC video streams.
I have a few discs that give me this same problem. Typically I rip to ISO, then extract with eac3to. If I get errors like you have, I re-rip the disc. It seems to be an issue with an unclean disc for me. It could also be a decryption issue, as I've seen a couple discs that re-downloaded the BK.bin after waiting a few days and re-ripping.
Eac3to seems to have much better logging than MkvToolNix. I usually use eac3to to demux, and mkvmerge to mux. If you're seeing 'sync byte missing' errors, re-rip the disc. If it continues, email Arusoft Support with the details.