I went to fight the Phoenix for the first time last night on my level 44 siren with Mayhem Mode Level 1 in Normal mode. It spawned, I killed its first form, it revived as normal, killed that, and then I died either during its third form (no other enemies in the area to get a second wind off of is a pain…) anyway, I came back in a vehicle, noticed I could shoot it with the vehicle from a distance, got its health low, hopped out, and shot it, and then it respawned again. After that, no matter what I tried, every time I killed it, it would respawn a level higher as legendary. It started as a level 45 Phoenix, and I gave up after it got to level 52. I left the map to despawn it and fought it again without dying and using guns/grenades only and it worked properly. So I don’t know if the glitch is triggered by dying, by using a vehicle weapon, or some combination of the two, or something else.
I think for those enemies that have stages, dying triggers the glitch. I had a similar problem with Mdm. Crawley - took her down to the point where she podded up and spawned the next two critters but died in the process. When I went back they simply weren’t there, but neither was Mdm. Crawley. I had to save-quit-restart and then start over (killing Mdm. Crawley again) to complete the quest.