We switched vehicle.teleportation to "true" in the settings.

Everytime we send a minecart through a portal, it will get teleported to the
"setto"-position, but always a little bit higher.
The issue after the 10th minecart or so is, that it'll jump from above 3 blocks or higher towards the rails on the other side.
I'll guess that the "setto"-position moves slightly higher and higher in altitude with every vehicle that moves through portals. Even players walking through that portal will end up teleported into the air.

We use AncientGates for our railroad-system on our server.

My opinion is, that
teleportutil.class add 0.5 height to a vehicle for teleporting safely,
the destination-point get's changed, but its height is not corrected afterwards by -0,5

Can you upload an explaining video? ;)

just send 20 Minecarts through a portal and walk through it after them.
You'll see that you got teleported not to the setto-position, but a few blocks higher.

Or you can make a portal and set the "setto-pos" behind it.
Now build a ring of rails from the "setto-position" around and back to the "setfrom-pos".
Set a furnace minecart on the rails, power it, and wait.
You'll see that it begins to hover higher and higher with every teleport.

wtf? xD

Here is the error AliensHive is talking about. We are getting the exact same error.

https://www.youtube.com/watch?v=IBWoxuWRcLQ

lol What black magic is this?!

Does the same thing for boats as well.

Look at TeleportUtil.java (line 295):
Code adds 0.5 to destination height.

This should be corrected after successful teleport, like adding:
final Location destination = GeometryUtil.addHeightToLocation(location, -0.5);