A user cannot check-in a document that is in a completed workflow.
When a document is checked-out, some actions can still be performed on the document. One possible reason a user is not able to check-in a document might be that a workflow starts. Then, the document is checked-out and the workflow completes. That puts the document in a state where the user does not have permission to check-out or check-in a document.
When checking out a document, try to be aware of a document in an in-progress workflow. There is an enhancement in place on the V17 release that prevents any state change on a document while it is checked-out.
Vault Help Documentation: Using Document Checkout
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