Well, most of us using an iPad and/or iPhone get the same mail on multiple devices.
So, the first, obvious thing to check is to see if the mail is also missing from the other devices.
Also, make sure you don't have a more sophisticated mail program set up on a PC, Mac, etc. that is moving mail from the inbox to specific folders. The mail might briefly appear in the inbox before it is moved.
In some cases (this is true for me, as I use Rackspace Mail) it's possible to actually have the server move messages to folders, based on headers and/or content. With RackSpace Mail, that mail never appears in the inbox, but with other similar server-based solutions, it might.
Finally, not quite on-topic, but keep in mind that new mail that appears in folders doesn't get counted in the iPhone/iPad "badges". Annoys the heck out of me, since I arrange to pre-sort most of my mail on the server.
Of course, everything I've said about "sorting mail into folders" applies to anti-spam solutions, as well. In some cases, mail that is flagged as spam might briefly appear in your inbox. So, check your junk folder. And, of course, make sure you are set-up to put spam in a folder, rather than immediately delete it.