What’s funny is that the most obvious side effect to this is the most realistic: molecular manipulation in this way causes an incredible build-up of energy that either expresses as kinetic or thermal, depending, and almost always exponentially explosive from the moment you turn time back “on”… to say nothing of the disastrous effects at the fringes for such time-stop powers…

tl;dr: The Flash would’ve incinerated the entire planet long before he discovered how to keep from glassing it simply by practicing his powers.