Sort of had the same type of problem starting off with seedlings. Come to find out a majority of the little brown spots came from nutrient burn after over feeding the plants with veg nutrients and using coast of Maine organic lobster compost plus organic worm castings.
New to growing as well and a majority of the problems that end up arising are just from over feeding while in veg. we cut back and used Ph balanced water for a little while and it did end up being the problem. After a few weeks we started to give them nutrients again while adding more worm castings and coast of Maine to the pots.
Try just watering with the Ph balanced water for a little bit and if possible there’s test kits out there for you to test the run off water that comes out from the bottom of your plants. If that doesn’t work they have the plant stress calculator on here so you can always try using that.
