There are 18 flags and each zone has 3.
Area 1: After motorcycles in beginning
Area 2-3: When you clear out the mass of infantry and 1 or 2 tanks area 2 will be cleared. After the bridge is some trees clear them out at the exact beginning of 3 to find a flag.
Area 5: Right after bridge in the beginning
Area 6: Behind destroyable rock on left before the dinosaur charge
Area 8: Right after first crunching walls on the left side before the second crunching walls.
Area 10: On the right side of the pathway near the beginning
Area 11: Midway through the mission on the right side. A tank comes from the left parallel to the flag.
Area 12: Where you get ambushed by a bunch of guys near middle to end of the area on top of the screen.
Area 14: Near end of bridge after going on foot.
Area 16: Middle of Asteroid shower
Area 18: Beginning of the map in middle of screen.
Area 20: Just after glass connector tube. It is at the beginning of the metal area.
Area 22: Beginning middle of square room
Area 23: Go down ramp it will be at top right of screen.
Area 25: After area on foot on the bottom right before you start heading north.
Area 26: At end of the 1st grated walkway heading east, just before going north it's on the bottom right of the screen.
Area 26: Just as you hit the dirt path heading on foot.
Area 28: In room on foot where the big zombie comes out just before clearing area 28. It is on the top right.