You say your chickens are flying over the fence? Have you clipped their wing feathers? That might be a deterrent till you get some more run space. (some folks offer a good argument against wing clipping, as it is a decision with drawbacks) there are instructions for how to clip, can be googled.
Lots of times young hens still don't have their adult weight, but have their adult feathers. And they can get some pretty good height with them. Some birds are just built slimmer, as well. Less weight, better flight.
Or, as a stop-gap measure, can you add some wire or even string about a foot up from the highest fence wire? Or string strung across the top, to give the illusion of a wire ceiling.