Corporate account with seperate locations all in the same account

Employee at a bank ($387MUSA)
We have a corporate client that had 3 separate accounts for 3 separate locations all using the same EIN. During the annual exemption review for CTR filing I discovered that they have requested that all of these accounts be condensed into one, which apparently we did. Now they are providing deposit slips to other locations and there are now 5 locations depositing into this one account. One of which may be an MSB. I don't see a legal reason why they can't all deposit into the same account but I'm having a problem that they can add locations without any due diligence just by providing deposit slips. I'm looking for others opinions on the matter.