There is an Inquisition codex update coming. So if there are some concerns they should be made on the digital editions facebook page. Concerning Allies though, it has been said by Eddie that the Inquisition can Ally with itself if the Inquisition is a primary, and an update will be made making it clear.
Other things I hope they clear up, psybolt ammunition, coteaz psyber eagle..... is there anything else?
via the Digital Editions Facebook page
You can ally two Inquisitorial forces together as long as one is your primary detachment.
There's an update on the way that clears up that confusion.
If you bought the eBook from Black Library, you can download an up to date copy from the 'My Downloads' section of your account now.
If you have an iBook one, it will update automatically soon.