"The Cartographer" Challenge uncompleted itself

I finished the final Precursor Tower in the fortress, my atlas tree has 311/311 points allocated, the "challenge completed" message showed up and I was at 5/8 challenges complete. However, as soon as I portaled out the challenge is now at 310/311 and my challenge log is at 4/8.
Something I think might be related is that "Defeat the Arbiter of Divinity to unlock" lock icon is still at the top of my tree despite me having defeated him 5 times, but this has not prevented me from allocating the locked passive points.

Interestingly, this seems to have resolved itself by acquiring a Breach atlas point.