Short answer: Something caused the drywell pneumatic valves to shut....the report doesn't state what that was, whether it was an equipment failure, a maintenance error, or an operator error. They were able to re-open the valves after the reactor scram, so an equipment failure seems unlikely, but who knows. Maybe they missed it, maybe they were fighting to get it back. This seems like it might have been a preventable/avoidable scram and could have been worse than it was from a post-transient standpoint.
Longer answer: The MSIVs are air operated to open, and a spring forces them to shut when they lose air. It can take anywhere from 5~10 minutes to an hour and a half after a loss of drywell pneumatic supply before the MSIVs start to go shut, it all depends on the leakage from the MSIV accumulators. My BWR's last loss of air took around 90 minutes for the last MSIV to go shut, but when we had high leakage on the air supply they've gone shut as fast as 5 minutes. I've also seen transients in the simulator in other BWRs where the drywell pneumatic valves go shut (usually happens at the same time you have other plant issues), and the operators miss it, and you end up getting an MSIV closure scram. If you just had a bus failure, or some other logic type issue, you may not see it. It also could have been a blown fuse on a drywell pneumatic valve, and they were trying to get it replaced prior to the MSIVs going closed?
Either the operators didn't know they were shut (seeing how they were able to relatively quickly re-open them after the scram, this may be what happened), or there was a malfunction they were fighting to fix and keep the plant online. They are lucky they didn't get all four MSIVs going shut. If they had done their power-uprate already, all four MSIVs would have gone shut (in uprated BWR plants, if 1 MSIV fails shut at full power, the increased steam flow through the other 3 MSIVs triggers the ruptured MSIV logic and shuts all MSIVs). But they could have ended up with all MSIVs shut and a loss of primary heat sink, using SRVs, drains, reactor water cleanup, and RCIC for pressure control.