there are two ways to link wtdoc. One is for the reference documents (this is a wtdoc subtype) and the other as described by.
They used to behave differently up to PDMLink 8. Then in 9.0 they added flexibility where both can be revised but one will remain at the version it was attached to, while the other type will be carried over.
I can't recall which one. I think it is the reference document which is carried over.
I would check which type of wtdoc you actually create and check which type you should be using.
Described By Links are Part Version to Document Version. You should use ECTs to Revise Parts and Described By Documents with the A-->B Revise button. If you do that from "Rev A" of the part and document as Affected Objects, then "Rev B" of those parts and documents only link to each other so that "Rev B" of the part does not carry over the link to "Rev A" of the Document. We do this for linked drawings.
Manual Revision of a WTPart will carry over a described by link to the new revision by default.
Manual "Actions-->Revise" from a WTPart Revision A with a Described By Link to a WTDocument Revision A results in a WTPart Revision B with a Described By Link to a WTDocument Revision A
However, if you attach a WTPart Revision A with a Described By Link to a WTDocument Revision A as Affected Objects on an ECT then you use the select-all, "A-->B" revise button in the Affected Objects section of the ECT than automatically Windchill will create WTPart Revision B with a Described By Link to a WTDocument Revision B as Resulting Objects on the same ECT.
Its very effective for managing Described By links, especially with CAD owner links where this is critical, but also with WTDocument Described By links.
As for Part Reference Links from Part to Document, those link a Part Version to a Document Master. You should not worry about those "carrying over" on a part revision since you would typically want a reference from revision A of a part to carry over revision B of a part by default, given the nature of most reference documents. If the link was "version specific" then you would have used a described by link.