Commonly reported issue. I don't know why apple took away the ability to control how many days or messages to sync for legacy POP accounts but they did.
Two known solutions at this point:
1) load ALL messages onto your device, mark them all as read. This is not what I would recommend.
2) go directly to the email server if you can, create a sub folder in the inbox and move all of your mail there, leaving just the mail you want it to pull down in the inbox. Close and open your mail app. It will autocorrect and show the correct number of read messages. From that point on it will keep 250 emails on your device and it should be resolved.
