When teleporting, the player triggers some pressure plates he doesn't stand on.
I don't know!? It's very random.
The only thing I can say:
1. make 2 squares from redstone lamps, one hovering 5 blocks or so above the other one.
2. Place pressure plates on all the redstone lamps.
3. teleport from corners to other corners . (I tried it without command blocks and then it didn't happen, where id did happen with command blocks)
4. Sometimes a pressure plate gets triggered on a corner where you haven't been.
Keep trying. It's very random, so you might want to try out very different coords.
Good luck fixing it, it's very annoying when you want to use different 'teleportation gates'. Sometimes you get teleported to a wrong location because you accidentally triggered a wrong pressure plate.