I received a 1099 but the income was actually deposited into my S corp account. What to do now?

Don't argue with them. Amend your taxes to show this income where they want it shown, and not as S Corp income. Decrease your reported S Corp income by the amount of these 1099's. Your total income stays the same, and you do not owe them any money. Problem solved. Much easier than trying to "prove" anything.