Reference in Reference List

We use EndNote X9 and maintain an online shared library at work.  We share the library with end users all end-users are provided read-only access to the library.  They cannot add or delete a reference in the library.  We have been noticing that the reference list in a document will have references listed that are not in our library at all.  How is it possible to have references technically cited correctly that are within to a document, cited in-text body, the reference is added to the references list correctly but it is not in our global library?

Thanks in advance