I have the same problem, actually! When I had my other bike, it didn't have the hollowed out cranks on the inside and it wasn't a problem. When I built this bike, I didn't even think of that being an issue... until I went to attach the magnet. Doh!
I don't know a solution. I thought about putting a piece of hard foam on the inside to take up the hollow place and zip-tie'ing it in place. Although I'm finding I don't even miss it (not like I thought I would).
I'm sure someone will have a good suggestion!