Duplicate of Issue ID #0016994 - according to the comments, possibly fixed in the latest dev build.

Running into this issue on a new mission I was creating. It is a stealth mission, where enemies would walk casually around town unalerted until you were detected, at which point they would become on alert (raise weapon) for a while. Since the release of the 'adapt' campaign, they always look like they are on alert since 'safe' combat behavior no longer works how it used to.