Same exact thing is happening to me and I'm not even done yet. I saw the scene with Greenhouse, I walked past the save point and it said something was unfinished, so i walked back to a random area, the usual glitchy chimera flew at me (it looked like Patricia) and.. nothing happened - then the bridge would let me pass without talking about being 'unfinished'. Then, downstream, Yaldukra says I saved him somehow. I'm thinking something bugged out and a scene was just.. skipped?
Reloading and trying my best to start the fight with it changed pretty much nothing, exact same problem over and over.