I'd have to say he's stepping on them. Either he's wearing shoes that aren't the right size or well fitted, and/or he's not moving correctly and/or he's overstriking. Do the shoes stick out on the inside or out the back? When he trots do you ever hear a click like the sound of him striking his front feet with the back ones?
New farrier?
I've been using this farrier about 6 months. It hasn't been a problem before. No clicking with movement. I haven't noticed seeing his shoes when his feet are down but I'll pay closer attention.