I don't reccomend doing this in the first place, but since it's a cool idea:
If you HAVE to do this, have like 20 tubes to almost completely remove that chance that two players will spawn in the same one and thus be teleported to the same place, and on being teleported use trigger_push or something to move them off the teleport spot so the players won't be teleported inside eachother
What eiii says works too, but then again what if it makes a tower as high as where the teleporter is and it ends up that two players get stuck inside eachother midair
There is no sure-fire way to fix this, you just have to take a number of steps to make it happening VERY unlikely, like a one in a million chance