Well they were relying on the Phalanx to totally annihilate everything infront of it. The other parts of the Alexandrian system suffered from neglect due to emphasis on phalangites and constant warfare. And by 'flanking,' people mean getting in between the blocks of phalangites (16x16 square of men), not the whole round trip of around the sides and rolling up the line.
I believe in the case of Cynoscephalae, the Romans literally ran into the Macedonian Camp in the fog and end up fighting up a mountain. The ensuing confusion caused part of the Macedonian Left to be disorganized. The Macedonian right formed up well and managed to push the Romans back. Infact, the right ended up throwing away their long pikes and going to their swords because the Romans were pushed onto some broken ground. The left however were in marching formation and the Roman elephants routed part of it. Then that Roman Tribune took those 20maniples behind the right and encircled them.
At Pydna, the phalanx hit broken terrain after initially driving the Romans off the field and gaps opened up. At that point the Romans just poured through the gaps and hit the phalanx from the side and behind.
Really it was a lack of cavalry to decisively win battles and reserve of more flexible infantry to plug gaps and defend the flanks of each phalangite block that caused the system to break down.
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