We are seeing this error too. I've created tracker ticket https://tracker.moodle.org/browse/MDL-60845
Two possible workarounds that worked for me:
1. If you turn on debugging, you can download the file. There will be an error message at the bottom, but it seems that all the data is there. The downside of this approach is that you need to enable debugging, which is a site-wide setting only available to administrators, and you wouldn't want this turned on in a production system.
2. In Firefox, from the page with the "File not found" error, you can right click and "View Page Source", which should show the file contents. Then right click again and "Save Page As...", and rename the file with the appropriate extension. The downside of this is that it doesn't work on all browsers (Chromium doesn't work; have not tried others).
Hope that helps,
Dom.