i'm guessing they were put there to ambush Avalanche as they got off the train, assuming they made it off of the train... President Shinra did know of the plans to attack the 'Sector 5 Reactor' and was waiting in ambush at the reactor itself, so maybe he posted several ambush squads along the train route in case they evaded capture and make it off the train, sort of a contingency plan... blowing up the reactor and Avalanche with it was probably his PlanB, as destroying the pillar was prolly PlanC, with each failure to capture or destroy Avalanche he would make the next attempt even more exreme...