I developed a staging site last week, then Cloned it yesterday. Aside from widgets not showing, Customizer theme options not copying, and a few other weirdnesses, it seemed to make it through well enough.
Then I got an email from a prospective organization member saying that an event URL had 404ed on her. I checked, and indeed, at least one recurring event isn't showing on the calendar. Screenshots of event settings and calendar attached.
I've updated the post and reset permalinks (because they were inexplicably changed when I Cloned the main site to staging).
An aside: This, combined with other short-fallings in the way Cloner appears to be built, make this VERY unpredictable software. Extensibility is a great goal, and has a lot of exciting prospects, but WPMU is not WP, and expecting lay-users to be able to hook into it—no matter how well documented the hooks are—is silly and counter-productive. Given Cloner is still promoted as a couple-click staging environment solution, I think that's false advertising.
I'm very surprised by the quality of this product from WPMU.