By analogy: there are at least something 10^34 (10 million billion billion billion) uranium atoms on earth, and they weren't explosive for billions of years, yet somehow they seem to be potentially quite explosive since 1945.
It's a question of critical mass. A small lithium ion battery may be safe, a large one may not be. Just because there are billions of tiny lithium ion batteries on the world that are relatively harmless doesn't mean large ones aren't - the energy capacity rises in the cube of the size, but heat dissipation only quadratically.
In short, because it works safely in the small doesn't mean it's easy to implement safely at scale.
