iMessage sent to one phone is going to another phone instead
Do they, somehow, use the same Apple ID? If so, the phone number has paired to the Apple ID, and every iMessage will notify the most active device (that is, the daughter in this case) before pinging the others.

As some would say, it's not a bug. It's a feature. I have a few solutions for your brother in law:

If the Apple ID belongs to the daughter

You said:


  she updated his phone and used her info


If the father has the daughter's Apple ID logged in on his iPhone, just go to Settings :: Messages :: Receive at on the father's iPhone and log in with the right Apple ID. 

If the Apple ID is the father's one

If both the daughter and the father are logged in to the father's Apple ID, you have the following options:

Get the daughter a personal iCloud account

As the daughter already has an iPhone, I suggest your brother in law creates an account for her. If they use a version older than iOS 8, they can go to Settings :: Messages and create an Apple ID from there that will just be used for iMessage and FaceTime. She will still be able to download apps from your brother in law account. Otherwise, if they use iOS 8, they can create a new child account that will be used for all services, including the App Store, but use the same credit card (the daughter will have to send requests to buy)

Disable the feature

If they have to keep the same iTunes account, you can go to Settings :: Messages :: Receive at on the daughter's iPhone, and uncheck your brother-in-law phone number. This way, she won't receive his iMessages anymore.