Not able to check in a document that was checked out by a Vault user.
The user who checked out the affected document no longer has View permission on that document.
If a user who checks out a document is removed from the Sharing Settings, that user loses View permission on the document. This user needs to be added back to the Sharing Settings in a lifecycle role that has View permission on the document. This allows the user to either Undo Checkout or check the document back into Vault.
Vault Versioning Documentation: Using Document Checkout