They sure can if they are too deep and lots of organic debris ( read as fish poo) gathers in one place. As R_Barber001 alludes to, plant roots will pump O2 in the substrate and prevent such anaerobic spots from forming.
I had an aquarium with sand and Crypts ( heavy root system) going for over 10 years with no visible anaerobic problems.
The anaerobic spots are more likely to develop later in the life of the aquarium (for organic poor substrate such as EcoComp. or Sand) as it compacts and gathers organic matter. Poking it is of little influence in my experience, it only helps to release the "poisonous" gasses forming under anaerobic conditions.