Star Trek, Transformers 2 and a few others have a more severe DVD protection system than others. This protection system (Made by Sony, called ARCCOSS) usually creates fake tracks (up to 99) on the DVD, and in some cases scrambles the scene order to trick DVD conversion tools such as DVD Catalyst. These DVDs also have issues on some stand-alone DVD players as well.
Installing the (free) DVD Catalyst Boosterpack can make some of these DVDs work, but the best way is to install a trial version of AnyDVD or to rip the problematic DVD to your harddisk with dvdfab

Only a very small percentage of DVDs have these issues.