Not sure if others are having this, but quite often I find units are not responding once I've given them a queue of things to do. I'll tell my engineer to build several metal extractors, but when I find enemies I'll try to withdraw or otherwise send a command. No luck, it just keeps building.
For engineers (and only engineers), early testers requested that they wanted the engineers to have to be ordered to stop before giving new orders so as not to inadvertently reorder their queued builds.
Discuss. 
I had noticed this too last night but quickly realised you had to stop them building before they responded to your commands but only realised this when i selected a lot of units at once when i was under attack but the engineers wouldnt be highlighted like the others and kept going on about their orders which i think is a good thing .
Not to bring up Sup Com again. But, the system they had is that Builder units would only be selected if you held shift with the click drag selection. Allowing you to select all combat units in an area without disrupting your builders. They would also be selected by a click drag if your box only contained builder units. I'm not saying you should copy that system but I believe it's a pretty good solution
Its interesting, but sill the best option is to give the Engineer some Kind of AI if they get hit to run away automatically or when they see the enemy at a certain radius will move back to the original location.
That needs to be togglable since the vast majority of the times when a fight is happening, i want my engineers to continue building defensive structures regardless of being hit.
As towards the original question, i believe the best option is the military units take priority during selection, with engineers being ignored. Took me a full game to understand why my engineers were not responding to my new orders, and whilst pressing stop does not take much, its not particularly intuitive either.
Shift drag is already in use to add the military units in the box to the current selection. But sounds a good idea with an other key.
Yes this is happend to me .
Almost every action i try to make with engeniers units or build dont react to my commands.
I have to click several times to make just 1 action, and then the pan view left mouse click, also isnt help , bit confusing.
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