F-Droid java.io.FileNotFoundException / won't update
What solved my problem was:


I realized, that 


the OwnCloud synchronization client is on version 1.7.2 on the webpage, 
while my F-Droid tries to download version 1.5.8
on the F-Droid webpage there is no version 1.5.8 for the OwnCloud client  
(which may have resulted in the "File not found" exception)

I forced my package sources/repository to reload 
(by changing my repository address to something invalid and back to original and then "update")
I could install the up-to-date OwnCloud client in version 1.7.3 (voila!)


Edit:

On F-Droid 0.96.1 it appears you can't edit existing repositories. You'll have to replace 2. above by


  
  I forced my package sources/repository to reload 
  (e.g. by removing the "F-Droid" archive (note the URL) and re-adding it)