Starting the level, take the west path from you, ignoring the down stairs, and open the door. Flip the switch (not the one requiring the red keycard), enter the tiny door it opens, go down the stairs completely, turn back and you will see that a small closet has opened at the far wall, containing a chaingunner. Kill him and quickly enter the closet before it closes again to get a berserker. Note: this secret triggers only once, if it is missed, it won't be possible to acheive 100% secret score.
A bit south of the northwest door of the "warehouse" (the huge indoor room full of crates, ladders and enemy ambushes) there is a small grey panelling on a wall. Activating this panelling reveals a switch. Throw this switch, then quickly return through the nearby door, go forward, turn right and you will see that one corner of the room is now opened for a limited time. Enter through this opening to access a closet with health bonuses and a plasma gun.