Hmm I think I know what's going on...
The path of the file being extracted is
\assets\structures\Economy\collectors_water\unique\struct_econ_cw_ar_water_j_connector_02_data\assets_structures_economy_collectors_water_unique_struct_econ_cw_ar_water_j_connector_02-collision.xmf
(pretty hueg

)
and I think most of you probably have steam installed to program files, so thats:
C:\Program Files (x86)\Steam\SteamApps\common\X Rebirth\extracted\
Putting them together makes:
C:\Program Files (x86)\Steam\SteamApps\common\X Rebirth\extracted\assets\structures\Economy\collectors_water\unique\struct_econ_cw_ar_water_j_connector_02_data\assets_structures_economy_collectors_water_unique_struct_econ_cw_ar_water_j_connector_02-collision.xmf
Which is a path with length 262 characters

The max length of a path in windows is 260 though afaik, guess that you'll have to copy the cat files somewhere else and then use the extractor...
I'll upload a new version now which'll warn you if the path is too long
Edit: actually I could probably just shrink the default path to \ext instead of \extracted, I'll add the warning too though