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I was creating plots in R with ggplots and faced the same problem (circles into squires). The suggested solution did not work for me, but a very easy one that worked was to change the transparency of the dots (for example alpha=0.2). Afterwards, AI does not read circles as text anymore and they are shown correctly!
This solution is so fast and easy, that I ...
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Fix the rounding effect. Apply Object > Expand Appearance before trying Shape Builder (or Unite).
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