This has happened a few times now and I am unsure on whether or not it is a bug with the mod or whether its a larger issue with the teleportation system in minecraft, but sometimes when I teleport to from one waystone to another, I end up like 3-5 blocks under where it should be teleporting me, causing me to start suffocating in a wall underground.

Does this still happen on recent versions (1.17/1.18)?

I have not had this in 1.18 so far.

just found this thread on google cause i had this happen on 1.19.4 in multiplayer. my guess is that the server is not sending the chunks fast enough so we start falling. maybe this could be fixed by freezing the player for x seconds after teleport if thats possible?

Regarding the "information needed" tag: I have had a similar thing happen. What appears to be happening is that your character's position is being updated before the destination chunk is fully loaded, so it doesn't think there is a block under you, and you start falling. Your Y coordinate is still updating, so when the world does finally load, you're buried alive and suffocating. I've had this happen in 1.12.2, as well as on 1.14.4, although the 1.14.4 version spit me back up onto the surface before I started taking damage.

Having this issue on my 1.16.1 modded singleplayer world. Strangely enough, I've had several other singleplayer worlds with this modpack that work, including this world; it only recently started doing this. It's mostly consistent in dropping me through the world, regardless of what position of waystone I use, and removing/replacing them doesn't seem to help. Is there any more information I can provide to help pin this down?