I have found out the reason why the unintentional spacing on articles keeps happening now. Turns out you're opening the visual editor first before heading to the source editor, because of that, the issues from the former are carried over to the latter. You need to set the source editor as your default editor when editing articles. Head to My Preferences > Editing > Editing experience > Preferred editor > Source editor > Save.
If you switched to the source editor as your default editor long ago, how come those spaces keep appearing? None of the editors who also have the source editor set experience this issue and it usually happens with new editors. The default visual editor and the visual view from the classic editor are pretty much the same thing, I tested both and both left those spaces, though only the former carried over the spaces to the source editor, that's why I asked you that.