We also experience this problem in a large multi-domain-installation. Trying to reproduce the bug in a smaller environment does not work out.
I will try to explain the bug a bit more and try to describe the behavior we found in our installation:
In folder /institute /Controlling/testdatei /
you find the file thisatest.zip – There are a couple of references to the file. The file has the ID 5261.
There is also a page with the same ID 5261. If you click on the references, you see that there are references to the file (correct behavior) and references to an images content element. If you try to edit the images content element, you see that inside this image someone has linked to a TYPO3-Page with the ID 5261. The references to the file are false. There is no link to the file, only to the TYPO3-Page with the same ID.
The correct behavior would be that only links, which point to the file are referenced to the file, not links that point to a page, which has the same ID as the file.
Can you fix this? TYPO3-Version is 6.2.