We have duplicated this issue 2X now on my BDS.  After the dragon fight, the Gateway to the End islands opens successfully.  We are able to traverse it, and begin to explore the end islands.  

After exploring the end islands and activating more gateways, the original gateway from the Dragon island to the outer islands stops functioning successfully.  Instead of teleporting back to the outer islands, it simply teleports you to a different location on the Dragon Island.

After this occurred, we completely reset the end and had this same issue happen after about 30 minutes of use on the newly  generated End.

In both instances, we were able to observe that multiple Gateways are getting stacked on top of eachother in the outer island.

1) Dragon killed

2) Gateway generated to outer islands

3) Explore End, locate additional gateways

4) Attempt to return from Dragon Island to End and the gateway fails.

5) Once a bridge is built and you return to the outer islands, you can see that there are now multiple Gateways stacked on top of eachother where the original return gateway was located.