The orange boxes indicate the positions of missing assets.
There are two ways of getting "rid" of them.
Find and download the missing assets (assuming they are on the DLS). CM will do this for you. Or
Open the Main Menu in Surveyor, select Settings then General Settings and unclick the box named Show Missing Assets. This does not solve problem because they will still be missing but you will not see the boxes.
They indicate there are missing assets at the location. Unfortunately, I don't think you can tell which are missing by clicking on them. Checking route and session dependencies will.