It really depends upon the extent of the imperfections
If the imperfect areas are relatively small and the mould is fairly flat in these areas, then you could key the surface and apply some additional gel coat (using a wax additive to ensure the gel cures tack-free, or cover the repaired areas with tape once the gel has been applied)
You'd then sand the repairs to blend-in with the surrounding areas and compound/polish
If you're only looking to make a single part with the mould, then you could fill the damage with filleting wax, but it can be tricky making it blend well with the surrounding areas. If your intended part will be made with an in-mould coating, this will permit a bit of flatting and polishing afterwards so the areas of the repair aren't so visible where the mould was wax covered.