I have had a few instances where some of my plants developed dark brown or black patches. If they remain small, about 1/4 to 3/4 inch and are small in comparison to the rest of the cactus, as they appear in your image, then I would leave them alone but keep my eye on them.

Sometimes when a cactus is taken from inside a store and placed outdoors, even a little direct sunlight can damage the plant if it is not used to it and can cause burnt patches, but I do not think this is what your plant is suffering from. I could be wrong.

for general growing conditions you might check
http://www.desert-tropicals.com/Plants/Cactaceae/Cereus_peruvianus.html

How often have you been watering it and have you been letting the soil dry out completely between waterings?

If the dark spots continue to grow and the underlying tissue is rotting and threatens to expand to the core of the plant you might want to cut the section off and apply a coating of sulfur to the remaining clean tissue.

I would also suggest you check both the plant and the roots for insects which can stress the plant. Root mealy bugs can destroy a plant and remain hidden from view as they do not live above the soil. A stressed plant may succumb to fungus or rot.