New single speed wheel and frame

I needed a new rear wheel for my single speed. It's a genius flyer.

The local bike shop stocks this bike and they said just bring the old wheel and they would build me a new one.

They built a freehub wheel rather than a freewheel which I only realised once I put it on.

Today I was changing the brake pads and noticed the wheel has done this to my frame. Is this normal or an issue?