Honestly, (unless your a true coral taxonomist) its pretty difficult to differienticate between these two species of Acropora 100%. The typical growth of A. prostrata is usually more vertical and resembles the growth pattern of a staghorn. The growth pattern of A. Milliepora is more dense and more clustered.- BUT- all of these growth characteristics vary according to environmental varibles- water flow/current dynamics especially.
In order to attain a more accurate ID look at the corallites, A. milliepora will have more protruding spaced out "scoops" for corallites - While, A. prostrata tends to have more compressed smaller "pinched" corallites compared to
A. milliepora
-corey