It's just a tiny difference in features of the apps, but that difference annoys you.
The Apple app will download at most n messages at first. If you delete a load it will download the next older (previously unseen) ones so you've always got at least n messages.
It sounds like the Android app just doesn't bother going back and getting you more messages if you delete a bunch of messages on your phone.
Some people will prefer the Apple behaviour. Some people will prefer the Android app behaviour.
I'm sure Apple's standard mail clients does support POP3, but there always were a myriad of settings, and as Kim says it was obsolete 10 years before it was conceived, so I'm surprised anyone is still using it. If they are, they should stop.
It does support POP3, but there are scant options. Having just checked I'm quite surprised there isn't an option in the Apple mail app to put a limit on the number/age of older messages it will download in this scenario (you can only control the minimum number of messages it will try and hold, leading to the 'download old messages' behaviour seen).
Other mail apps exist for iPhone though, those will almost certainly be more configurable. As others have said, Apple designs its own things for the vast majority of users with an eye on simplicity.
But, as others have said, this is all an artefact of POP3 mail. IMAP is vastly superior and obviates the need for any of this nonsense and/or a billion and one configuration options.