need to retrieve older version of product assembly

Might take some work, depending on the complexity of the assembly structure.

Do you have checkout when downloaded enabled? This may be preventing some files from being downloaded if Windchill is set to not allow check out of older iterations.

Try downloading sub-assemblies first, then any parts before the top level assembly.

The most fundamental "responsibility" of the CAD Data Management part of PLM is to be able to retrieve and use (and republish if needed) the As Stored condition of all data.

Is there any CAD message when opening the data that may give a clue to more specifics of what is "messed up?"

It's a long shot, but I'm wondering if the permissions are set up such that the user retrieving the data does not have access to a state at which at least some data in the As Stored list is currently at.

Would be worth comparing the result for the current user vs. an admin which for sure has access to all states.

It's also possible that one or more Revisions of the data was moved to a different context that the current user does not have Read / Download access to.

Note: You can test this fully from a browser without CAD to start.  Enable the tab "Relationship Report."  Choose latest and then As Stored and export the results to a file for both users, then compare.