A brown box appears when something exists in a city for which a dependent model file is missing. Brown boxes can occur on lots, or in flora/MMPs. The best solution to a brown box is typically to query the box to find the name of the lot or flora, then check to make sure that all of the dependencies for that lot or flora are located in your plugins folder.
A mod has been made by Pegasus that replaces the brown box visual with an RGB icon. Because these are smaller than the brown box, this mod can make it easier to figure out which part of a lot is missing its model.