In MSys2 Fish and ZSh run with the latest MSYS connector there is an extra symbol on every drawing of prompt (see screenshots below, in each case prompt function is empty, i.e. doesn't draw anything by itself). In ZSh it's just a %, while in Fish you can see that it's a return-key sign.
Maybe it doesn't render properly when it receives no newline character or something (I remember seeing this symbol when trying printf commands that didn't send a newline char), but not really sure.
Strangely enough, in Bash no such symbol is displayed.
ConEmu 160313 
ConEmu cygwin/msys connector version 0.7.4 set MSYSTEM=MINGW64 & %ConEmuDir%\..\msys64\usr\bin\conemu-msys2-64.exe /usr/bin/zsh -l -i
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Yep, realized later on after my comment ;)
Great project by the way! I was trying to ask Mintty author to implement a simple Ctrl-C/V to copy&paste remapping and he was very resistant referencing some stupid 30-year-old standard (even though top terminals in Linux allow you to happily remap copy&paste to ^C/V and move interrupt/next line sequences to another keybind, e.g. Ctrl-Shift-C or something).
But gladly I can just use your awesome connector and not remember for just one use-case that copy&paste is mapped to something else vs. all my other apps.