The overlay with t value has precedence over other overlays. If the problem
occurs, I can run the following function, and it will get fixed in existing
windows. However if I create a new window, it will show only text. If I
press + in that window, a new overlay will be created. Perhaps the t
overlay was meant to be the default, and someone misunderstood it's effect.

(defun 13887-fix-helper1 ()
  (interactive)
  (let* ((ovs (overlays-at (point)))
         (ov-t (find-if (lambda (ov) (eq (overlay-get ov 'window) t))
                        ovs)))
    (when ov-t (delete-overlay ov-t))))

Here is one more helper function which might be useful.

(defun 13887-own-overlay-present-p ()
  (interactive)
  (let* ((ovs (overlays-at (point))))
    (find-if (lambda (ov) (eq (overlay-get ov 'window)
                              (selected-window)))
             ovs)))