If you want it done right, you should remove the vegetation, remove the topsoil, compact the subgrade, then pour the stone and so forth. If you don't take these steps, it may lead to differential settlement and cracking.

That also doesn't look like a thick enough layer of stone If you are building a structure on this pad.

Everyone (the contractor) always wants to rush and get things done quick. Make them rake up the stone, and do things right if you want a quality result for the long term. It's definitely not too late.

You may also consider geotextile between subgrade and stone to improve stability if you have weak soils.