Issues arise from the end of the first fight, where the "filled" exit portal is summoned two blocks above the "empty" portal that was present during the fight. This has been reproduced in every save file I have tried it in.

With subsequent kills of the dragon, portals continue to be raised (see screenshot 1, screenshot 2), and the dragon egg is spawned repeatedly, even if broken (screenshot 3, taken after a dragon kill after screenshot 1). In addition, an end gate spawns with each death of the dragon (screenshot 4). I am not certain whether or not the repeat dragon eggs and end gates issue is a bug or an intended feature, but I was under the impression that both only spawn from the first fight. Regardless, the portal being raised does not seem to be intended.

EDIT: The end gates take you to different locations, and one pair of end gates will only link between the two. This begins to seem more like a feature.