i @jmerriam another penny's worth on top of @Chris_Hofer and @NoahBoswell ,
I found today that when I used "Copy To' for an assignment it failed to transpose the links to the new course, despite the links being set up correctly - we know this because the transpose worked fine using 'Import'.
There are instances where specific copy tools (like Copy To) need to include all the resources that are linked - so if everything is organised as a link in a page, all those items are added to the module block with the page, and the whole module block copied.
Overall my instincts is that @NoahBoswell is on the right track, and you may have legacy links that were created in a different way to the course and file links in RCE etc.