A really interesting concept! I'd love to see what kind of puzzles you could introduce with it :)
I think by nature this physics sim can get really chaotic with so many forces acting on each other, often I'd have magnets flying all over the place. It might be possible to alleviate this with more simulation steps or maybe a max velocity that the objects can move at?
The only major bug I found was when viewing at a low angle and moving objects with left click, I'd send them far off into the distance as there's no level bounding box.
Overall, a super interesting and ambitious concept! I'd really like to see what you can do with it :) Great stuff