using git-annex 6.20180807-23 on Arch I get this message from time to time:

 copy archive/Studium/Diplomarbeit/Daten/Vortrag/vortrag.snm (to xgm...) 
 git-annex-shell: <stdin>: hGetChar: illegal operation (handle is closed)ok
 copy archive/Studium/Diplomarbeit/Daten/Wheels/SingleWheelCalcs/5SpokeWheel/5Spoke_MRF/6000/Lambda2.gz 
   Lost connection (fd:21: hFlush: resource vanished (Broken pipe))
 (fd:21: hClose: resource vanished (Broken pipe)) failed

The peer is git-annex, downloaded at Aug 7 at Debian Stable. Repeating the file transfer makes the message goes away, but I have to initiate the transfer multiple times, to be able to transfer all files without this error message.

Best Thanks!