What causes these spots?

Looks like the PH fluxed a bit to me, but I agree with other in that this plant is overwatered and it looks like its been this way for some times. Adopt some better watering standards, its hard to understand but if you know you like to poor lots of water in then amending with more perlite might be a better option as it makes it hard to over water, granted you will need to water more often when the plants are bigger or setup an auto watering system and drain tray. As for PH, let your solution sit out fully mixed for 12 hrs and test its PH, see if it is stable it might have drifted a bit. With soil its good to aim for 6.2-6.5 for PH range in the soil. It can also hold onto a lot of nutrients so be carefull of overfeeding it as it does not flush well. Good Luck!