It's far too easy to accidentally pop wrinklers, upgrade buildings, or cast spells during a Cookie Storm. Even clicking on a mundane Golden or Wrath cookie over a Wrinkler always causes a wrinkler-click, even if that's not enough to pop them, which makes me nervous.
Ideally there'd be some kind of overlay so that you cannot interact with anything but the Big Cookie left of the Store during a Cookie Storm, but the fact that the Storm doesn't overlay the Store indicates Orteil understood the mis-click problem... then added things to click underneath the Cookie Storm area anyway.
Some form of "open / close" mechanic for the buildings, like for the Grimoire and Pantheon, that protects the Level Up buttons would go a long way. And perhaps Wrinklers should "shelter" under the Big Cookie during the Cookie Storm or something.