The mail "threads" changed in iOS 10, placing the oldest message at the top of the list. Most people prefer to have access to the most recent email first, then scroll down to read previous emails in the same thread. It can be troublesome to scroll through large blocks of text just to find the most recent email. To resolve the issue:
Go to Settings > Mail. Under the Threading section, turn on "Most Recent Message on Top". This will place the newest email in the thread on top with the rest of the emails in reverse-chronological order.