Here's an arbitrary example that (on my system) behaves as you describe:

$SIG{CHLD} = sub { wait };

system "date && foo 2>/dev/null";

print "ret: $?\n";
print "err: $!\n";

_END__
Tue Jan 10 17:19:35 CET 2012
ret: -1
err: No child processes
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The -1 is because of the failed foo. and the "no child processes" (ECHILD) is because of the SIGCHLD reaper getting called without there being an unreaped child process (system() itself has already reaped it).

As you haven't shown what exactly you're doing, I'll leave it up to you to check for possible similarities with your code...