If you've found rogue RVT links in your model it might be Transfer Project Standards (TPS) and View Templates to blame. When you need a View Template from that other project you're working on you run the risk of adding RVT links to the project's database. You'll find them listed in the Manage Links dialog but if you try to reload them Revit will tell you there aren't any instances placed.
This happens when a View Template manages overrides to those linked RVT files in "that other" project. Just remember to check Manage Links after using TPS (reports, haha); otherwise this Gotcha will Getcha.
Hat tip to Alexis Kotzambasis for identifying this issue.