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My desktop betta, Jetta, is prone to those little pinholes in his fins. I have determined, through help from the kind folks here, that they are "blowouts" from flaring. They always heal within a couple of days and don't seem to cause him any discomfort. It sounds like you have a good cleaning schedule and nice warm water for him, so that's really all he needs to heal if it is indeed a flaring blowout. Jetta gets them every once in a while - maybe every other month or so.
