Two different faculty have encounters this problem in two different places.

One was editing the Text Comment on assignment feedback.

One was editing a topic summary.

They would click on the link option, then click Browse Repositories, then select Upload a file.

They would upload a file.   

The link would be fine initially, but later when editing the text again it would sometimes get changed to reference "brokenfile.php" rather than the "pluginfile.php".