Bukkit

Due to the way the plugin maintains height, if you build a portal around height 125 in the normal world and travel to the nether, not only do you end up being able to access the upper half (which I don't mind personally - but may be an issue for others), the portal also replaces the bedrock.

Not sure you'd consider this a bug as the plugin does exactly what it's meant to do, but some would argue that it shouldn't send you to the upper half of the nether and/or replace bedrock.

I actually like the fact that it sends you above the nether, my players can use that as a sort of 'safe travel' dimension.  My concern is that they'll use it to destroy the bedrock barrier between the two halves though.

It didn't use to do this - if you set height: 128 in worlds.yml for the Nether world, does it still happen?

128 seems to set it straight, but it also cuts off access to the top half of the nether. I just started getting used to the idea of letting players access that area, but I haven't officially introduced it so it's no big deal and I can live with it.

Is it possible your code only checks that the top blocks of the newly generated portal are going to replace bedrock?

Nope, it just adjusts the maximum height for the world based on if it's Nether or not. If it's a Nether dimension it considers the max height to be 5 lower or something. Detecting bedrock would be smarter but take more effort/code, this is a simple if (destWorld is Nether) { maxHeight -= 5; } :P