Yes i know that but if i have to do that every time that they do not take cover then for me it would take the fun of playing the game away. I just hate being the babysitter and that i have to take care of my squadmates every time they do not take care of themselves and take cover.
What you can do on the "warehouse-like" side missions is order your squad to stay just by the door (in cover on either side of it - in ME1, both squaddies will go to the same side of the door) in the "lobby" room, then advance into the room with the enemies by yourself. When you get the attention of the enemies, run back into the "lobby" and take cover on the side of the door opposite your squad. Some of the enemies will follow you and your squad will start taking them out as they come through the "tunnel" that adjoins the two rooms. When enemies stop coming, just repeat the order to your squad to stay in cover by the door and go back in to attract more enemies to follow you back to the door. Repeat until the enemies are all down.
As I've said, the squad AI does improve in ME2 and again in ME3; so you can take heart in that. Also, if you level up your squad mates right, they really will not go down that often even though they don't take cover well. Level them up to have high levels of health, immunity, barrier, shield boost, and regeneration and then give them as good an armor as you can find and upgrade that armor with a "first aid" interface (which you'll find in chests early game), a "medical interface" (mid-game find) and a "medical exoskeleton" (found later once you're leveled up enough to start finding level 8, 9 and 10 gear). You can also buy some medical upgrades from Dr. Michel on the Citadel if you're not finding them. The tech squaddies don't have regeneration in their skill trees, so you have to give it to them via their armor upgrades and their omni-tool upgrades. The later omni-tool upgrades (e.g. Savant X) will give them a significant health regeneration boost... but you don't tend to start finding them until after you've hit Level 49 or so. The Bring Down the Sky DLC (if done after you hit Level 49) will often yield a Savant IX or X omni-tool upgrade.
There is a lot of learning involved when it comes to tailoring your squad mates skill trees to your Shepard and learning to use each squad mate's talents to their best effect. Tali is a GREAT squad mate for geth and drones (because of AI Hacking); but she can also be very effective using Sabotage on organic enemies and she can kill a lot of husks with an upgraded shotgun. I know you're on casual and probably using the "active" setting for your squad's talents. This means that they have a tendency to expend their whole skill suite right off the bat when the enemies first show up. It is actually much better to put the squad setting on "Defense Only." This means they will activate their defensive skills on their own (barrier, immunity, etc.) but will not use up their offensive skills. That way, when you want, say, a hack or a throw from your squad mate against a particular enemy, it will not be on cooldown when you go to order it.
One thing you also have to think about is that if you put your squad mate's too much behind cover, they cannot shoot enemies for you, but instead get bogged down shooting into the cover that's protecting them. If you want them helping you eliminate enemies, you do need to have them getting out of cover to do that.