After a lot of play I've found all of the secret missions.
here they are.
The Exorcist, Mission 3 - 15th Avenue. Examine door on the right hand side of street
Untouchable, Mission 5 - Surge of Fortunas. Examine the red skull.
Death from Above, Mission 7 - Dark Corridor. Behind torch, examine the red statue.
Devil's Teeter-Totter, Mission 8 - Surge of Fortunas. Examine the red skull.
Destroyer, Mission 9 / 10- Examine Red Crystals in Limestone Caverns.
Flight of the Demon, Mission 10 - Behind and to the right of the Neo-Generator's location.
Hang 10, Mission 11 - Examine Red Seal on the wall in the Gears of Madness.
Tough Guys, Mission 12 - Examine the odd object in the Underground Arena.
Target Practice, Mission 13 - Vestibule. Examine red eyed skull above the blue torch.
Guiding Light, Mission 16 - Golden Sun Chamber. Golden door next to altar.
On Pins and Needles, Mission 17 - Pitch Black Void. Examine glowing statue on bottom rafters.
Final Ascension, Mission 18 - Road to Despair. Left side of giant foot statue
Hope this helps!!!