watering fluctuations can be a factor but so can calcium. When you pot up container tomatoes you usually want to mix in some lime. If you have a hydroponics store near you I would recommend you pick up a cal/mag supplement and follow the package directions. I personally use 1 tbs molasses per a gallon of water and use that as it contains calcium, magnesium, iron, and some trace elements.
Either one should help fix the BER issues. Though I am sure some others will also have other alternative treatments that will also work equally as well.
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