This is something I had noticed yesterday when starting to play for the first time, it took me a while to figure out why my units wouldn't actually shoot, and then continue to get slaughtered. As it turns out when some units and building were built, they had the 'hold fire' order pre-selected, rather than the more useful 'fire at will' Some construction buildings also had this problem too, however am I right in thinking if the construction buildings have this order, those orders will be passed down to the units it build?
I can't find my source, but one of the devs said that the system isn't actually implemented all your seeing is a visual placeholder. Your units aren't set to hold fire they are set to fire at will.
http://forums.uberent.com/forums/viewtopic.php?p=739436#p739436 Some posts down you can see Ben posted something about it. <mod edit: change link to go directly to post>