Some programs (e.g ssh when asking for a password) write directly to the terminal, not STDOUT.

$ ssh ikegami@209.197.123.153 2>&1 >/dev/null
ikegami@209.197.123.153's password:
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You have to create pseudo-tty's (as Expect does) in that case.

IPC::Run supports capturing STDOUT and STDERR separately, and easily. It even supports pseudo-tty creation if you need them.