They very fact that they were banged together by an intelligent agency makes them a tool.
No it doesn't. When I was a child (ostensibly an "intelligent agency") I was known to bang rocks together but it certainly didn't make them tools - not in any meaningful sense of the word. For something to be a tool it has to have a functional purpose.
In general you can tell by close examination whether a potential tool is simply the product of natural erosion or in fact was used as a tool.
Quite correct. However I've had the same doubts being discussed here regarding whether certain rocks really were used as tools or not. I'm not an expert so I don't pretend to know the answer but I've seen "tools" in museums which made me wonder if the people who collected them really knew what they were doing. Call it skepticism even though I don't really know what I'm talking about on the subject. I tend to be skeptical about things by default until I understand them.