This problem occurs if your world border in the Ultra Space is lesser than the one set in the overworld. For example, let's say that the world border in the Ultra Space is set to 5,000 blocks, and the one in the overworld is set to 12,500 blocks. If you enter a wormhole while at X=7,500 and Z=2,300 in the overworld, you will get sent to these approximative coordinates in the Ultra Space even though it's way past the world border set for that dimension. As a result, you will promptly die if in survival, and unwanted chunks will be generated in that location.

What the game should try to do when entering Ultra Space is substract your X and Z coordinates until both of them are lesser than the Ultra Space's world border. If I retake the example above, it should substract the X coordinate from 7,500 to 5,000 while leaving the Z coordinate at 2,300 since it's not higher than 5,000. This is what happen in regular Minecraft when you exit the Nether from a location that would normally send you outside of the overworld's border.

I was able to confirm this and I have sent this off to the team so it can be put into the internal tracker. Will update when I receive info on this matter.

I'm not entirely sure what the status here is, but I've just moved it to internal. Keep an eye on the ticket status to see what's up!

This is actually the case with Other dimension of vanilla minecraft as well. It happens with the Nether too. Of course it would be a blessing if it was at least fixed for Pixelmons dimension though !