Prevent movie being split into parts?

[Uxorious]

I've got an issue with the BD release of Shogun.
It's a 3-part release, on 3 disks.
Disk 1-2 ripped fine, but for some reason Disk 3 wants to split the title into 2 parts.
During parsing of the disk, it writes:
File 00000.mpls was added as title #0
File 00000.mpls(1) was added as title #1

I guess I can merge the 2 files afterwards, but why would it split it in the first place - and is there some way to prevent/edit it?

[Woodstock]

It's been YEARS since I ripped Shogun, and that was on DVD, but I think the 3rd disk has two alternate cuts. I just chose one and went with it (I think the longer of the two).