Sounds like a poorly constructed package. That said, be aware that what we see as duplicates are probably a lender requirement.
Loan documentation goes through many different departments, and internal audit requirements widely differ. For instance: Accounting may need an original note, Compliance certainly will, etc.
This company may be using a secondary source of funding, such as a larger bank, Freddie Mac, or a venture capital firm. In that instance, multiple signed originals would be required of the note, ID verification, and whatever other docs each company involved in funding needed to satisfy their own internal audit procedures.
Multiple copies of the same docs are generally not included to simple frustrate the NSA.