Are they any other famous atmospheric explosions besides the Tunguska Event? It need not be "strictly" an explosion in the atmosphere, just that it requires an explosion of some sort. ( No Hiroshima, Nagasaki, Chernobyl, other nuclear disasters please.)
Such events are not particularly common. If you are looking for past events to blame on your alien wars, I think you're only going to alienate your readers. I know I groan whenever the Bermuda Triangle is dragged into a story as a time warp nexus.
What I had in mind was that these (Tunguska Event, The Missing 9th Roman Legion, etc.) were battles fought over the millenia-long conflict.
There are books simply entitled The Unexplained and things like this. Sounds like you might like to read up on those. There could be a wealth of info for you.