Is this when you first start a game? If so, then serious bug! But not one I've encountered.
If this is during a game session you have to remember that spawning in the same region means alert status won't have changed and you WILL be chased if seen... also the "safe" rebel hideouts are anything but "safe"!
If you get a chance, disengage and as soon as you've lost contact fast travel to a point outside that region. Per session alert status' carry on (as far as I can tell) meaning if you're spotted you will get chased even if you've not done anything recently and even when there is no active alert status up.