Take this game; why is present on the Android Market but not on AppBrain?
The reason can be find in AppBrain FAQ:
4.I cannot find some apps, what's going on?
It always says "The requested item could not be found". AppBrain lists applications that are available in the US that are available for Android version 1.6 and up for devices with a normal screen size. Developers can restrict availability of apps by country, Android version and screen size. This means that if you're not in the USA, have a device with a small screen size (for instance the HTC Wildfire or Tattoo), or when you're not on the latest version of Android, you may often get the "not found" message from the Android market.
So, to give you an example, I am a developer and published an app on Android Market, that is restricted to France and Germany, so users from those country will find it on Android Market, but not on AppBrain, who lists only US applications.