what does this mean on facebook?

[Jacob]

"Alex is using an app to chat. To message Alex, you need to change your settings to let friends who use apps see if you're online. Would you like to allow friends using other apps to see your online state?"

I recently changed my privacy settings so that friends apps couldn't include me as I don't like too much invasion of privacy ... as I've heard some people can use an app to see how many times you've viewed your profile etc. Now what I want to know is this app that the person is using in the aforementioned part ... they probably would use a dodgy app that's why I'm asking, can it see when I'm on fb but turned of chat... any ideas what this is guys would be great as I don't want to allow it if it's dodgy!