This may be related to this bug: https://forum.inaturalist.org/t/renders-as-br-in-observation-comments-ids/17361
However, I’m not aware of any version of Markdown that gives a special meaning to a row of tildes. Two tildes are generally used for strikethrough font (coded as ~~strikethrough~~). Regardless of how it’s supposed to be interpreted, the <br /> should never show in the final rendering.