Hopefully the contents of said alert weren't important, but in most cases I'll never know…
If any one application emits multiple notifications (say, several new calendar items), they pop up in a group -- but this is hard to see, since they're all stacked on top of one another. There is an X at the top-left corner, just like all other notifications. When you go to click the X, the group suddenly expands, and the X changes into a "Clear All" button!! 80% of the time this results in me closing a large stack of notifications without realizing they even existed.
However, that unfortunately doesn't help with in-app notifications/alerts.