Kyla, you're right, most herbs are resistant to bugs and fungi because of the aromatic oils in the leaves.
Your spotty situation is very mysterious! Did you try a little soapy water on some of them? (tell your roommate which ones you spray with it, so she can rinse them off before she dries them).
The other thing to try that is somewhat preventative, and non-toxic is a solution of baking soda and water, 1/2 tsp. soda in a quart spray bottle. If the cause is a fungus, the baking soda spray will prevent it from continuing to spread.
As you say, it doesn't seem to be doing much harm to the plants overall, and they're going to start winding down pretty soon.
