Not entirely sure, but an interesting test case I found is the following:

perl -e 'print `echo test`; print $!."\n";'

shows $! to be empty. I am guessing the issue is that echo is attempting to output to a non-existent terminal, and this error is a result of an internal perl call to determine if the output is being piped to an existing terminal. Note that

perl -e 'print $res = `echo test`; print $!."\n";'

does yield $! eq "Bad file descriptor".