Reproduction with emacs -Q:

(with-current-buffer (get-buffer-create "*broken*")
  (require 'cl-lib)
  (erase-buffer)
  (delete-all-overlays)
  (fundamental-mode)
  (insert "AAAAA")
  (goto-char (point-min))

  ;; Add two faces
  (set-text-properties (point-min) (point-max) '(face font-lock-type-face))
  (let ((ov (make-overlay (point-min) (point-max))))
    (overlay-put ov 'face 'font-lock-negation-char-face))

  ;; This passes, proving that font-lock-negation-char-face is not contributing to the
  ;; foreground color
  (cl-assert (eq (face-attribute 'font-lock-negation-char-face :foreground)
                 'unspecified))

  ;; This fails: foreground-color-at-point reads the face of the overlay, sees that it's undefined, 
  ;; and ignores the 'face text property 
  (cl-assert (eq (foreground-color-at-point)
                 (face-attribute 'font-lock-type-face :foreground)))

  (pop-to-buffer (current-buffer)))

Let me know if I can provide more info.
Clément.