If you look at the Cygwin.bat file you have this line
bash --login -i
Starting Cygwin this way yields expected results
$ cat ~/foo.sh
cat -v <<< ~
$ ~/foo.sh
/home/Steven
However if you change the line in Cygwin.bat to this
bash -i
it produces unexpected results
$ ~/foo.sh
/home/Steve0^G
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