I doubt it's as simple as two companies failing to pool resources. Cross Cult do use Pocket Books covers for many of their books. The reasons they might make their own at other times could be many, and certainly not limited to them simply not liking some of the less impressive Pocket covers - They are catering to a different market with different tastes. They are often publishing their versions of books years after the originals, so might want to model a new cover on what they think will work in the current market, not designs of years ago. Plus I imagine there's at least a little bit of it being about getting publicity; they get to make a bit of a fuss when they reveal a new cover design, so more people will hear about their books as a result.
So any money saved by not making two cover designs is I'm sure carefully balanced against the benefits of paying out to make something new. Plus it's not like Pocket can't make good covers on their own; I'd say Pocket and Cross Cult have similar hit and miss rates.