The colored squares (or rectangles) in the upper left corner of a map sector indicate that there are enemy (or friendly) aircraft in that sector flying over 200ft above ground level. The larger the rectangle, the more planes in the sector. If you haven't reset the map colors, those "Sector Counters" or "Bar Dar" will be red (enemy) or green (friendly). Remember, the aircraft can be anywhere in the map sector -- not just in the top left corner where the colored square is. (Map sectors are 25 miles square and are outlined in white, with coordinates in the lower left corner.)
The red squares that can appear anywhere in a sector are "Vehicle Sectors" that indicate there are one (or more) enemy vehicles within the square. The Vehicle Sectors DO indicate the approximate location of the vehicle, but not the number of vehicles in the square. (You can enable/disable the Vehicle Sectors by right-clicking the map and checking the appropriate box.) On water, the Vehicle Sectors indicate the approximate location of an enemy LVT or PT Boat.
