Try shooting with small aperture against a bright blue sky. Does it show up?
If so, it's probably something on / to do with the sensor. If there is dust on a sensor, then that shows up as dark/black spots, and also only at narrow apertures.
Your spots seem to be more see-through and may be caused by some liquid that dripped on the sensor (internal lubricant?). Set the camera to manual clean (have it lock up the mirror) and see if you can spot anything suspicious on the sensor surface. If there is something, you might want to clean your sensor or have it cleaned.