Test::Harness does not care about STDERR.

C:\>more bad-test.t
warn "1..22\n";
warn "not ok 22\n";
print "1..5\n";
print "ok 1\n";
print "ok 5\n";
print "ok 2\n";
print "ok 3\n";
print "ok 4\n";

C:\>prove bad-test.t
bad-test....1..22
not ok 22
bad-test....ok 3/5Confused test output: test 3 answered after test 5
bad-test....ok 4/5Test output counter mismatch [test 4]
bad-test....ok 5/5Test output counter mismatch [test 5]
bad-test....ok
All tests successful.
Files=1, Tests=5,  0 wallclock secs ( 0.00 cusr +  0.00 csys =  0.00 C
+PU)

C:\>
[download]

So if you system child is printing to STDOUT, there could be trouble.