No the reason for Messene & Rhegion would've to be found with the existence of a landbrigde (to stimulate the AI to conquer Sicily; specifically if it is SPQR) -- or in other words the immediate limitations of the RTW engine.

You will find this to be the case with some cities in the Greek Mainland as well-most notably the location of the Akropolis of Athens outside the stratmap city of Athens.