Hiya

With order handling capacity you can limit your standard MFN orders to send in one day however, additional orders are still counted but with an extra day’s prep given.

For SFP (seller-fulfilled Prime) there is a Control Prime Order Volume feature in general shipping settings to set the capacity limit for your Prime orders.

BUT Amazon do say… Quote:-

<<At certain times, the orders that need to be fulfilled on any given ship day might exceed the daily limit set by you. This happens because customers might store the product in their cart and place an order at a later point of the day or week.>>

I guess this is what has happened to you.