Autopsy on fully clothed Alex : A Web of Intrigue video mentions that everything on Alex is actually part of his biomass, this also explains how he mimics people and their clothes repeatedly and discards them for his own form, and repeats this as often as he wants to. It also conveniently removes a nude scene and the source of his clothing during his escape.
People running around on the streets while the infection spreads (not escaping) : the island is in quarantine, though the seemingly oblivious behaviour of the pedestrians few blocks away is not explained by this, nor why they don't hide indoors.
Infection detectors not triggering for the soldiers themselves : presumably adjusted to ignore minor cases of infection, though apparently not mentioned anywhere. In truth, it's likely an oversight from the developers.
People running around on the streets while the infection spreads (not escaping) : the island is in quarantine, though the seemingly oblivious behaviour of the pedestrians few blocks away is not explained by this, nor why they don't hide indoors.
Infection detectors not triggering for the soldiers themselves : presumably adjusted to ignore minor cases of infection, though apparently not mentioned anywhere. In truth, it's likely an oversight from the developers.