If two apps register the same custom URL scheme, it is undefined which app will actually be launched. One will be launched but there is no way to know.
Here's a real kicker. If you have two apps on your device with the same URL scheme, and you delete the one that actually gets launched, the other one will not get launched by the URL without rebooting the iOS device.
Your best solution is to ensure your custom URL scheme is not trivial so there is little chance another app will have the same scheme.