I was having the same problem just try doing the objectives nearby by like disable the generators even though it has nothing to do with aegis but while you have aegis active, and return to see if it works. Also try driving away then coming back. You have to kill everything around before it let's you activate even though it shows it shooting/active you can still activate it after you kill everything. When it shows press E or equivelent try killing everything nearby. If it doesn't show it drive away then return until it shows it when it does kill everything and it will let you.
Ive almost finished all side mission and finished main story, I gotta say there was 3 bugged mission, but then I joined to PVP, came back and it worked in every time. Nothing to complain really, if you think how many damn quest there is.