I don't think there was any intentional significance of A or B by the residents of Terminus.
The facility appears to be a factory of some sort with multiple buildings and "A" and "B" are merely their respective identifications.
Maybe "B" building is where they process the "meat".....
As they are running, Gareth shouts “Get them off B!”, which to me implies that there is an “A” path and a “B” path. The “A” path is clearly marked and apparently leads to the boxcar trap. Not sure where the “B” path leads, but Gareth didn’t want them on it.