I can't state this with 100% certainty, but it has been my experience. And I have seen a couple of similar comments on reddit.
I started this nightwave a few weeks in, and spent a weekend working my way back through the first couple weeks. Multiple times I would complete an act or 2 then have only 2 or 1 showing. After traveling to my dojo or doing a mission most of the time 3 would show again. I got down to 1 challenge, thought I should have more based on my calculations. Tried traveling and didn't get one, then tried relogging and that worked. I did a similar thing a couple weeks later. I have since been playing a kind of week on/week off since hitting 30 and multiple times have found relogging worked to show me 3 acts.
It's possible that is doesn't always work, or that some acts are bugged, but it's a least worth a try.