Well, it wasn't built to send people through gates, but is it truly a malfunction? I think a big question we have to decide here is what really happened. First off, are we assuming that the telepod shot power through the pendant, which in turn opened the gate? In that case, there's a big discrepancy, which of course will be immediately answered with "gameplay mechanics". Lucca and Taban aren't really shoving as much power through the pendant when it's around Marle's neck, yet with Crono they have to, in some terminology, "force" it back open with a large amount of power?
As far as malfunctions go, do we say that CT is a malfunctioning product because someone figured out you can fight the Black Omen in 1000 A.D....then 600 AD...then 12000 BC? No, it's an oversight on the part of the programmers. Is a game that you can play over the internet malfunctioning because a low-level player has high-end equipment or has exhaustive amounts of gil just because a friend sent it to him? Nah. (Trust me, I play Final Fantasy XI and I always get people calling Square-Enix on me because I'm curing my girlfriend's character whose about 50 levels below me...that's not cheating, it's using the game mechanics to our advantage when the company knows what is going on and chooses not to do anything about it.)
Or here's one: Lead. I know this was brought up. Lead has been around for the longest time, that is, known to humankind. So has Gamma Radiation. But when you realize that a thick piece of lead can actually decrease the amount of gamma radiation received, it's not the originally intended purpose of lead. So do we say lead is malfunctioning by preventing Gamma radiation?