For clarification this was on running on a 1.15.2 bukkit server, with McMMO, however I doubt this would have effected my issue.

I was fighting the ender dragon as I normally do, running around on the pillars breaking the crystals and placing water buckets on the top so they flow down. However half way through I noticed that the ender dragon got stuck flying underground in a roughly 30 block radius under the water, you could only see his wings and somethings the rest of his body above the endstone. He continued to fly in a figure 8 pattern between two pillars that were submerged in water so the ender dragon was under water the entire time. After destroying all the crystals I attempted to free the ender dragon by removing the water buckets. After removing the water the dragon immediately broke out of the loop.