I had queued a whole lot of apps in F-Droid from the main page that has the most recently updated apps and was in the process of downloading them over Wifi.
Then I did search for Orbot and clicked download.
F-Droid crashed, somehow deleting my queue and now all downloads give the Connection refused error, even apps that I had not already queued.
I have sent in the error email after both crashes from the email address attached to this forum account, however it was the second crash that caused the queue to disappear and all new download requests to fail.
I had a decent look through the Issues Tracker but I did not find a matching error.