often in early game only one team colour is shown on screen at a time. This is usually the colour of team which has had a unit enter screen most recently. All units on screen are only of one team colour. This mean the colours will flash back and forth when panning across a area of map where there are various teams .
Occasionally it will go even weirder where for example yellow and green have bases close to each other and green base will have alternating green and yellow units and yellow base will have the same. Then if you move the screen slightly all will go yellow then move it some more all will go green.
This does not apply to radar map only to units rendered team colour.