I'm having trouble figuring out exactly what the timeframe on this was, but for a while in November we were not writing edges between pastes and their attached files correctly.
An example of this on this install is here:
https://secure.phabricator.com/P1893
That will start working once the migration runs, but until it does it shows this:
This got fixed so recent stuff works fine, but it looks like WMF updated while the bug was active so they have more affected pastes than we do (we only have about 10).