Lancaster and the doc??? Why?? Also,Lancaster assured EVERYBODY would be killed, so the remaining "soldiers" will kill survivors, anyway?? Isn't the plague going to pass down the damn river????
Well, to answer the 'thread' question first, Col. McKenzie and the doctor are under surveillance for their knowledge of the bio-weapon/virus. Rather, that such a weapon was being engineered by the US in an int'l organization on foreign soil, and a neutral country no less.
This is a just a thought. Anyway, there could be other reasons for the surveillance, such as their involvement in what happened to the train and its passengers.
As for the other questions, the soldiers' chain of command has broken down, esp. as their leaders (on the the train that is, including some guy named Scott) were killed either in the bridge collapse or in the passengers' brief 'rebellion'. Plus the troops at this point seem more concerned about saving themselves than following orders.
As for the plague getting in the river, most of the passengers seemed unaffected by the virus, or else were getting better due to the oxygenated environment on the train (or whatever explanation the film gives for that). Still, there will probably be a bio-team around to mop up the mess. There's also no indication that the virus traveled to that part of the train anyway.
In the novelization, which is worth a read, the authorities held the survivors at the bridge site and then put them in quarantine for 45 days and brainwashed them into not revealing the true fate of the Transcontinental(!!??) Express.
I think there would have been much confusion after Navarro in the movie shot out the radio unit in the baggage/mail coach when he was holding everyone hostage while high on drugs as well - who do they take orders from . . . tho Scott seemed to have an upper hand.