Not knowing the particulars of each incidence that you speak of with your
VLBW babies, but if I were guessing, I bet there were fortifiers,MCT oil,
and all kinds of things ordered to be added to the EBM of these babies. 
Smelly stools isn't something to be concerned about in most cases. The
feeding intolerances would probably occur in some babies no matter what they
are fed just due to the fact that their GI systems are so fragile.  All
breastmilk will culture positive for something- after all, it is a living
substance and we all have bacteria on our skin that can't be "sterilized".
Depending on the brand of pumps you are using, most cannot harbor bacteria
in them and if they did, the bacteria would have to find it's way up tubing
and past protective one way valves in most cases. I also work in a Level III
NICU and we never have any of the things occur that you're speaking about. 
Our neonatologists do require a 7 day "quarantine" in the freezer on EBM of
mothers whose CMV status is not known or if the babies are VLBW. 

Hopefully, you can do a controlled study on what is going on in your NICU,
consult you infection control dept for assistance, and get some answers to
some of your concerns.  I would venture to guess if any contamination is
occuring, it is in the storage, handling, or administration of the milk to
the infants if it is indeed breastmilk related.  

I would never suggest that these moms discard their milk.  Freeze and save for the baby when not so fragile at the very least!

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