I just discovered that when I view the events on www.icloud.com the ones that are improperly alerting for me show up there with the alert option turned on, even though they don't show as alerting on the macs or ios devices. So far, it seems that turning off the alert on www.icloud.com fixes the event on the icloud server (so it won't get sent to all the devices). It doesn't fix the cause. That's something Apple has to figure out.
But I think it's related somehow to the mac Calendar Preferences Alerts options. In the latest Lion, either someone has Events>At Time Of Event as their preference, or the default of None is not working. On each mac, try toggling that preference to some value you don't want, like 5 minutes before, then close and reopen preference and turn it back to None.
I haven't tried the toggling method, but I have checked icloud.com and at the time there were no events turned on. On Sunday, I physically checked every event in every cal for the week and so far there has been at least 5 alerts that come in at the time of the event. Actually, I've been noticing they arrive after the event even though when you check they're marked at 0 mins. I've run programs like iCal Cleaner which do set alerts back to none, but they are still showing up anyways.
Im super at a loss about what to do. There is no logic to the cal within iCloud that these alerts are happening, type of event, or time of day.