That's quite an awkward discovery. I think you should approach the situation calmly. Try to start a conversation with him in a non - accusatory way, like 'I noticed you near my shoes and it made me a bit uncomfortable. Is there a reason?' This gives him a chance to come clean. If he doesn't have a good reason, it might be a sign of a more concerning behavior, and you may need to distance yourself from him gradually.
Well, that's a really strange situation. You could just be straightforward and ask him why he was doing that. He might be embarrassed and give you a valid explanation like he was looking for something that dropped near your shoes and accidentally got too close. If not, you might want to keep your shoes in a more private place away from him in the future.