You have to understand the difference between the movie mode and the fiel mode.
File mode copy the data as if you were copying whatever kind of files on your PC. It does not look into the files to see what is inside.
The IFO (or movie) mode use the PGC (program group cell) to know what it has to copy.
99% of the time, the PGC follow the vobs in a linear way. But sometimes (when you have angles for instance) the PGC do not follow the vobs. And in this case the problem you had occurs Logan.
I had the same thing once on a DVD with cartoons. The main and end titles that is normally read at the begining and end of each episode was in fact only ONCE on the DVD. There were in the cells 1 and 2. The cartoons episode were in 3, 4, 5, 6...
So the PGC was : 1,3,2,1,4,2,1,5,2...
This is really tricky sometimes
And I do not even mention tricks used by producer to make the copy more difficult (like "Finding Nemo" where there are false cells declared in the PGC).