An uncontrolled document is one whose content is no longer controlled in accord with the security standards of an organization. Document management systems have existed for several decades (see A Machine-based Document System, written by M. R. Powell in 1962 or a book about Lockheed's document management system published in 1987), and they may be paper-based, digital, or both.
The precise definitions of uncontrolled document vary from organization to organization, but in general the label suggests that the document is not credible or reliable for use, especially in sensitive operations. For example, Samaritan Health Services defines a controlled document and specifies it cannot be used when providing service guidance:
A document that was removed from or never part of the controlled document system. Uncontrolled documents may not be used to provide service direction or information necessary for the performance of service. Examples of uncontrolled documents are
training aides and informal communication tools.
And NASA gives this definition, specifying printing or duplication:
Uncontrolled Copies. Those that are printed from the Master List
system or duplications of the signed hard-copy document.
As you've experienced, organizations may choose to release copies of documents in an uncontrolled format with an explicit label. Their rules may also designate documents as uncontrolled even when not labeled.