In order to use the end portals (not the End Exit/Entrance portal, but the outer island portals) in a slightly different way, in previous versions I had constructed a room around the portal and filled it with water. I was able to swim into the portals to use them instead of throwing ender pearls – they worked beautifully.

However, since the 1.9.0 update, when I swim into these "water portals" I made, the destination portal always traps me in a standing position, with my head inside a bedrock block, slowly dying while warping back and forth between the portals. It is like many episodes of Star Trek where they attempt to beam someone up but they become trapped in the transporter beam and they see parts of both worlds back and forth until they eventually horrifically lose them and they die somewhere.

The only way to successfully get out was to throw ender pearls away at every angle I could until I finally warped into the water. In doing so, it destroys the portal block completely.

Can this be fixed? Being trapped inside a portal isn't fun.

This is easy to reproduce:

Build a 7x7 block room around the portal with a floor level with the bottom bedrock block and a ceiling level with the top bedrock block and 4 complete walls. Fill it completely with water, leaving an escape hatch on the side or top to get out/in. Go through the portal and construct an identical room on the destination portal. Swim/sprint into one of the portals and begin suffocation while unable to escape the transporter beam.