I recently made a mould out of glass fibre and resin and then finished it off with acrylic rattle can spray paint but after vacuuming my carbon fibre project it turned out to be a disaster.
I waxed the mould several times before applying the resin and laying the carbon fibre and then vacuum bagged it. It wasn't the easiest to release and it left an imprint on the moulds surface from the carbon fibre and ruined the product I pulled out.
Can someone tell me what I have done wrong and how I can rectify the problem? 

Theoretically yes, but in reality no. You will never get that surface flat again, especially with gelcoats or resins. You'll lose your dimensions and it won't work.