Why does undergoing Agnes treatment leave brown and red marks/ spots behind?

Please do not continue with home remedies for your acne, as a lot of such remedies are completely unsubstantiated, and may often cause more harm than benefits. The burn marks you’ve experienced are probably due to the acidic nature of vinegar, possibly having been left on your skin for too long. This will recover with time, and leave behind some post inflammatory hyperpigmentation (PIH). PIH is probably also what you described to be the mole-like spots left behind by acne.

I usually combine different treatments for such cases. This include topicals, oral medications and machine driven treatment. For your case, besides topical antibiotics, oral Isotretinoin (eg. Oratane) will be worth considering in combination with machine-driven treatment such as lasers. Agnes also targets acne via Radiofrequency energy but is not a permanent cure for acne. Do have a consult with your doctor so that an appropriate treatment plan can be tailored to your needs. Hope that helps. All the best!