I can't say I've seen any issues like that on any commerical discs I've watched before.
It could be that the correct display format hasn't been set properly in the DVD's ifo files. You can use IfoEdit to check and correct those if necessary, per the guide here:
Using IfoEdit: Setting the 16:9 Flag
If you load up the MKV files in mkvmerge GUI, I'm sure you can also set the aspect ratio or display format from one of the tabs.
IfoEdit will overwrite the DVD files on your hard drive when you execute the changes. mkv merge however will create a whole new file.