Charged twice for CGT?

Submitted my SA and paid early. Realised I needed to declare CGT although this had been paid separately. Went into SA and amended it, but have now received a statement wanting more money, as if CGT hadn't been paid already.

Hi,
If you have corrected the return to take into account the CGT already paid, any amounts still due on the Self Assessment record will be in relation to the other entries in your return.
Thank you.