Thanks for reporting that! It's because those scenes use the same scripts (and so do Sion's scenes at least on Malachor and possibly elsewhere, it would have broken them to). I was supposed to use the TSLPatcher to install them but I wasn't thinking, sorry!
Anyway, this will happen with both versions of the mod. If anyone else is experiencing this, your options are: put the files into the override folder only after Sion's kolto tank scene and remove them after you escape the Harbinger OR remove the files and install v1.1 that will use the TSLPatcher and be up very soon!
EDIT: The mod is updated! Sorry for the inconvenience!