Looks like maybe a micronutrient deficiency, or an overwatering issue to me.

I agree with Peter. Also overwatering + nutrient deficiency go hand-in-hand, since too much water can leach nutrients out of soils.

For rust the brown spots are usually larger and more distinct, with a small yellow halo around them, and if you looked on the other side there'd be more brown + powdery brown spores there as well.

If it were virus only other legumes would be in danger, and I'm pretty sure that's the case for rust too. There are a whole lot of species of rust and most of them are very particular about what species they'll infect. For example a couple years ago I had some that went to town on my lima beans but left the neighboring snap beans untouched.

Rust isn't generally a big deal, at least what I get. I get it every year.