Secret #1
There is a part of the level where there is decompression and you need to hurry to a safe area. During this process, you will reach a bunch of chairs in rows. Pass the FIRST set of chairs, and you will see a cutscene. Once the large explosion occurs, the wall will be torn open to the south. If you go south instead of north (away from the exit direction) you will find the Secret on the floor in the far top left corner. Here is a screenshot of the location I took.
http://steamproxy.net/sharedfiles/filedetails/?id=382589946

Secret #2
You will reach a room with two blue electrical bolts above your head. You need to shoot some explosive canisters that you will find in a small tunnel near this area. Shooting these canisters will blow open a wall where you will find a corridor of wires and moving pistons. Follow the path to the end to find the Secret on the floor. This hall is BEFORE the mandatory area you will come across later that looks the same. Here is a screenshot of the location I took.
http://steamproxy.net/sharedfiles/filedetails/?id=381582357

Secret #3
Near the end of the map there will be a section where the life support system is failing and there will be a 10 minute timer. First off, don't worry about the timer, it's all bells and whistles and doesn't matter since the ship already crash landed I imagine.
Once you get up and out of the water and reach the other side, explore the platform and you will find a couple explosive canisters close to a large box that says "Dislodge Point" or something like that. Activate this dislodge point and you will kick the box and observe the canisters roll down towards some boxes in a hall. Go back down to the area where these canisters ended up and blow them up. Now you can go down this hall, and you will find a key card.Take the keycard to the locked door where you can see the Secret, and use the key card.
Here is a screenshot I took of the door you use the keycard and the Secret.
http://steamproxy.net/sharedfiles/filedetails/?id=383142675

Secret #4
You will reach a point in the map where there will be a console you can use over and over. A short distance from this area is a locked door. Inside you can see Hardened Armour, some ammo and the Secret. The "Operationals Console" opens this door for 6 seconds. You need to activate the console and then run into the door before it locks up again. It's not too difficult.
Here is a screenshot I took of the room where the secret is.
http://steamproxy.net/sharedfiles/filedetails/?id=385088890

Secret #5
After the first Boss Battle with the Alien Queen, use the "Elevator Console Switch" where the Queen was standing on, near her bleeding tail to activate two elevators to your left and right. The elevator on your left will lead to the secret. Take a look at your radar here and just head away from the goal marker.
Here are a couple screenshots I took of the direction you need to go from the Alien Queen Tail, and the Secret.
http://steamproxy.net/sharedfiles/filedetails/?id=431893190

http://steamproxy.net/sharedfiles/filedetails/?id=431893406