i dont know if transporter malfunctions are a plot device, but the alternate "goatee" dimension has been usd a few times, and ds9 used the transporter to time travel a couple of times.
theres the "captain gets wisked off the bridge to fight an alien"
and "parts of the crew get wisked off to fight another group of whatevers" ... but those are usually caused by powerfull aliens or whatnot so...