On my system, Ubuntu 14.04 with fish as my default shell, I get the same
problem.  The problem can be reproduced with a much simpler vim command
":r! ls".

I can work around the problem with the following (fish command)
    env SHELL=/bin/bash vim

FYI, on my system, my default shell is set by the chsh command and is
stored in /etc/passwd.

My uneducated guess is that vim is expecting the shell it calls to be
bash or Bourne shell compatible and fish is not compatible enough to
understand what vim is telling it.

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