I have several email accounts, all with Virgin, and one with Hotmail. I have it set up so that all my mails download to both my Mac and my iPhone. The last few days, I've noticed that one of my email accounts is not receiving mails on my iPhone, although they are still appearing on my Mac. Other emails are coming through on my iPhone just fine, it's just the one account.
I've not changed my settings recently in any way, except to update to iOS 6.0.1. I have iPhone 4.