I don't know of an app for that, but it is worth improving. If you can't find an app that does what you want, try simplifying what you're doing until you know you're locked in with the metronome. Just simple strumming on every click and nothing else. Even eliminate the guitar entirely if you have to and tap on your desk or something. Then gradually add complexity back in while making sure you're locked in at every step.

There's also an exercise I remember Victor Wooten talking about where he would have a click track or something to that effect that would cut out for a measure every once in a while. The idea is that if your timing is good enough, you'll be on the beat when the click comes back in. You could set up something like that in Garage Band. Make the gap small at first and then gradually increase it.