In the American Campaign in the mission where you first gain access to using Oil with the secondary objective in finding the second oil reserve (I believe it was mission 3 or 4) I was taking my time with it slowly building up my strength.
I got to a point where my defenses were mowing down Russian Infantry and their vehicles would get damaged too quickly for them to escape before being forced out and killed allowing me to repair and steal for myself.
Where the second group of soldiers arrive from the EON I was slowly capturing the Russian base there so I could transport the crates back to my main base and recycle everything, as I was doing the guy in command (I think it's Morrison) complained that I was taking too long and took control from me. All my soldiers in their turrets at my base got out, my scientists and engineers inside their building at my base got out and my engineer at the Russian base stopped work and EVERYBODY rushed the main Russian base, suffice to say I lost an engineer and scientist. There would have been more casualties if I hadn't have so many vehicles.
Now I was putting up with that whining about taking too long for a while now because I figured these were just objective reminders and I had the time to properly prepare for the final push (do some drive-by on the defenses, have everyone in a vehicle, making sure no one got killed by having an effective withdrawal plan) but this got me wondering, are there any other missions that steal control away from you if you "take too long"? If so, what signs can I look for for when this happens?