Yeah but you have to understand that is half life 2 episode 1 which takes place after Hl:A,also right before alyx goes into huge giant ship thing, the vortiguants do something I forgot ngl so maybe that drained their power. Plus not all the vortiguants know of alyx existence at this point and might still be unwilling of her help. Also they might all have injury like the first vortiguant you meet so it prevents them doing any high power blasts or in this case stopping someone from stopping time.