When I first saw these, I naturally assumed they were caused by insects. But, not necessarily.
Closer observation: You cant rub or clean them off. They are visible from the top when light shines through too, so it looks more like a deformity than a pest. Sometimes they look like white salt or sugar grains, sometimes clear bumps, and sometimes a bit brown.
There's a thing called "oedema" that plants can get, the main cause of which is overwatering, or rather, waterlogging. I certainly think that's it for me, because I chose badly with soil, I ended up with a sandy soil that holds water for days like wet cement. Unfortunately its too late, but I'll learn for next year.
Anyway - it's not too bad. I guess the cure is to water with less volume, don't soak the soil as much.
More info, including photos, here
http://apps.rhs.org.uk/advicesearch/profile.aspx?PID=637
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