Check the logs: when Prussia DOWs Austria, does Austria also DOW Prussia? If so, it's because you're declaring on the same minor.
I suspect that's the cause, because from what I've seen, Prussia is (in 1.04) much better disposed to ally with Austria against France, as it should be. BUT it is also very aggressive about German minors, and I have several times seen it DOW Bavaria right away, which is ridiculous. If you went after Bavaria also, that would trigger the war, but then (as above) you should see a *mutual* DOW.
On the Napoleon casualty, that's weird. I haven't seen that, so it may be just coincidence. I will say that I've seen more leader deaths in general than I would expect. (Should be 1/216 combats, I think, but it seems more frequent; I can't prove that, though.)