So, decided to try a scratch removal cream, which I've never thought worked. What it has done, is shown up the stone chips on the bonnet, even after using a wax polish I can still see them, it looks like the scratch remover has filled the chips in. The colour is anthracite so they show up more. Any remedies please.

What you'll have is the polish (scratch remover is just a coarse polish) within the chip. Having a dark car it will show up even more due to the contrasting colours. To remove the polish from the chips use a tooth brush to clean them out and some IPA. 

Fill in chips with paint, sand flat and polish, which is basically the same rule for any kind of paint defect that you can catch a nail on.

If you want to temporary fill the chips use coloured polish or wax, even a wax crayon. 

Thanks CWARD. IPA ? sorry its my age.

Rubbing alcohol 

 

https://www.amazon.co.uk/500ml-Isopropyl-Alcohol-pure-ISOPROPANOL/dp/B00AMZ10SE

 

not India Pale Ale. Although the later tastes much better.

 

 

Isopropyl alcohol.

 

Personally i would just buy Indian Pale Ale, put a little in some polish and use on the chip and drink the rest with fish and chips and tartar sauce.