With regard to the iOS 9 POP email bug, it apparently was caused by an intentional change made by Apple, which breaks every single rationale behind using POP instead of IMAP.
They are now treating mail on the iOS device as transient in cache, eligible for removal at any time. Their presumption is that the mail will be downloaded again from the server whenever next accessed. In other words, they expect POP to behave like IMAP.
So if you delete mail from the POP server, then the mails previously downloaded to the iOS device will not be retrievable if and when they get removed from cache on the device.
I use POP because I want my local copies to remain accessible on the device forever, even when isolated from a network. And once mail has been retrieved by my "master" platform (my Mac), then my mail client deletes it from the server, as is expected with POP, so that I'm not constrained by inadequate storage limits on the server.
That is the way POP should work, and until iOS 9 it did work that way in the Apple world. Now, iOS 9 treats locally cached mails as disposable, expecting them to be available forever on the POP server. Very very wrong.
I have filed a bug report with Apple, but I'm not terribly optimistic. They've apparently decided that the POP model is wrong, and that they'll not accommodate it.