The proximate answer is that your shoes at the closest point, are too close to the crank arm, but that hardly solves your problem!
This distance is affected by a large number of factors: your cleat position, pedal axel length, pedal float, bottom bracket length, and crank arm construction.
Pedal float becomes a factor if you heel-in during your pedal stroke (some peoples hips naturally make them "duck-footed." In this case a longer pedal axel or shifting the cleats to a more inboard position can help. However shifting the cleats too far can also cause hot spots in some situations as the pedal platform will not be supporting the shoe as evenly as a more centred position.
Too add to the confusion people may also take a duck footed position to compensate for pedal stance (often referred to as the Q Factor), the distance between the pedal attachment point and the centre of the bicycle. Q Factor is a function of both the bottom bracket width (axle length) and the crank arms construction. Different cranks have a different nominal Q Factor measurements. If your bike has a wide Q Factor and your body prefers a more narrow stance, and your pedals have enough float to accommodate, you may pedal heel-in to reduce the realized stance, which can also cause the shoe/crank rubbing.
Finally, you may be pedalling in a mostly neutral heel position and simply have wide feet and short pedal axels and/or an outboard cleat position. In this case a more neutral cleat position (inboard vs outboard) or longer pedal axel may solve the problem.
Without more information it is impossible to diagnose which factors are applicable to your situation.