I reckon this happens sometimes while adding a link using the "insert hyperlink" tool (either by clicking the button or pressing Ctrl+L) instead of using Markdown.
The input box contains https:// (which is selected) by default
(and I believe it used to have http:// by default previously). So usually while pasting the link, it overwrites the https:// with ...
The problem seems to be caused by copying a link with a preceding space into the Insert Hyperlink dialog. The software adds http:// in front of it and a broken link starting with http://%20https:// is born.
See What causes “http://%20https://” links to be made? on Meta.SE for details.