I can think of a couple of potential scenarios causing this behaviour:
Firstly when you add a Site Content type to a list/library it basically creates a copy of that site content type in the list and it becomes a List Content type, new columns can be added to this list content type completely independently of the Site Content type, so its possible that this rogue column has been added directly to the List Content Type and may have a default value set?
You can check this by looking at the content type from the Library Settings page.
Secondly the Content Type that is currently associated to a particular item doesn't necessarily prevent a value being set on a column that is not part of that content type.
Every column added to a list is technically available to any item in the list.
The SharePoint UI just makes it difficult to alter values in these other columns not associated with the current content type, but not impossible. Perhaps the rogue column is a calculated column, which depending on the calculation involved may always get a value? If this is the case you could refine the calculation, or remove the column from the list.