Since Overkill updates their Bundle Asset format in order to increase update and installation downtime, it screws up how Bundle Modder read the file.
And as a result it can't extract asset properly anymore.

As it's unlikely that Bundle Modder will receive updates/fixes from the creator, 
for now Frankelstner have alternative way to make Bundle Modder work with the new asset format

Read more here:
https://steamcommunity.com/app/218620/discussions/15/1474221865204158003/