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I am not able to make the MKV for the main movie with the MI5: Rogue Nation DVD.
I turned on debug logging and it is generating this log:
MakeMKV v1.10.2 win(x64-release) started
...
<snip/>
...
DEBUG: Code 233 at 6PCbhHbR07vsZAITtbf8uJ4h:0
Operation successfully completed
Saving 1 titles into directory D:/Movies
Error 'Scsi error - ILLEGAL REQUEST:ILLEGAL MODE FOR THIS TRACK' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1608898560'
Error 'Scsi error - ILLEGAL REQUEST:ILLEGAL MODE FOR THIS TRACK' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1608898560'
DEBUG: Code 101016576 at 0*u53V?r+$wd$Pq.aI:121262969
Error 'Scsi error - ILLEGAL REQUEST:ILLEGAL MODE FOR THIS TRACK' occurred while reading '/VIDEO_TS/VTS_05_1.VOB' at offset '1608898560'
DEBUG: Code 0 at 8=h{tZTtt133Ig!gb;mX:121263291
DEBUG: Code 0 at DxIJT?6Nhc_=P66"\8e:121261750
DEBUG: Code 0 at 8=h{tZTtt133Ig!gb;mX:213130812
DEBUG: Code 785595 at 8=h{tZTtt133Ig!gb;mX:29393286
DEBUG: Code 0 at T:}L'Aj<w&w(~v+!IEKR(:29398967
LIBMKV_TRACE: Exception: Error while reading input
Failed to save title 0 to file D:/Movies/title00.mkv
0 titles saved, 1 failed

Any ideas?

I'd recommend starting with cleaning the disk. If the problem persists, follow the FAQ in my signature to submit the necessary information to Mike to see if it is an issue with MakeMKV itself. He may request additional information.

Thank you for the advice!
I was able to rip the movie with WinX DVD, so I didn't think to check the disk itself.
Looking more closely at the disk though, I see what looks like a defect that could explain the problem.

It turns out that WinX DVD probably had the same problem and ripped only 2/3rd of the movie, but didn't tell me there was a problem.

Looks like a disk defect.