The red dot might be from the CodeMirror v6 highlightSpecialChars extension. By default, it replaces several invisible characters (e.g. zero-width spaces) with a placeholder.
Before the recent updates, Joplin desktop used CodeMirror 5 by default, which may have replaced a different set of special characters. For example, CodeMirror 5 shows a red dot instead of a null character, but might not show a replacement character in other circumstances where CodeMirror 6 does.
Note: For comparison, it's possible to re-enable the CodeMirror 5 editor in settings > general > advanced.