Not sure about the alien NPCs, but I do know from looking through the .dlg files that not every party member's dialog is completely centralized within their own dialog file. A few are located elsewhere, in other character's dialog files. In any case, you won't believe how much dialog is tied up to your party members. A messed up copy of the dialog file for one character will have great impact on a most of that character's speeches.
In either case, it is most likely a mod problem of some sort if taking out those .dlg files made a difference. I am curious, though, as to the name of the mod that caused this problem.
- Star Admiral