Jake,
I don't know if you are still looking into this problem, but I just used the choice module today and it was set to only two choices per option. The limit didn't work and one option had six people select it. This time separate groups was turned on and the students were allowed to update their choices. We are using Moodle 3.4.1+ (Build: 20180228) and the choice is build 2017111300.
The one similarity to previous issues was the students (not a large number) were making choices roughly at the same time. I uploaded a screenshot of the logs that I exported. You can see the times when they made their choices. Choice id 313 was the one that was selected six times instead of being limited to 2.
