they are root nodules (aka root primordia) basically, it wants to send out more roots from the stem when there is present of moisture. nothing to worry about.

Thank you! But is it normal for them to flatten out and turn brownish? They aren't really bumps but are more like scales.

This is what I have. Doesn't really fit with any of the common diseases. Did you the spots/scaling continue up the stem to the branches and kill your plant?

I don't recall them killing the plants. They did much better when they went outside into the garden though.