Yes, the AP discounts does not work at a number of locations where non-Disney vendors sell items. The full text from the AP site:
"Discount is not accepted at Walt Disney World® Resort Operating Participant locations, including but not limited to, China, Japan, and Morocco Pavilions at World Showcase in Epcot, Arribas Brothers, Basin®, Basin White, Cirque du Soleil®, Curl" by Sammy Duvall, Ghirardelli® Ice Cream & Chocolate Shop, House of Blues®, Hoypoloi,
LEGO Imagination Center®, Niki Bryan Spas, ORLANDO HARLEY-DAVIDSON®, Planet Hollywood®, Rainforest Café®, Richard Petty Driving Experience, Rubio Balloon Arts, SD Watersports, Sosa Family Cigars, LittleMissMatched®, Sunglass Icon®, Surrey Bike Rentals, T-Rex® Café, Wyland Galleries, The
Disney Store, Disney's Character Premiere, Disney's Character Warehouse, and any other locations or kiosks that are not owned and operated by the owners of Walt Disney World® Resort. Discount is not valid at the Bibbidi Bobbidi Boutique or The Pirates League and is not valid on purchases of ticket media, gift certificates, Disney Gift Cards, videos, DVD's and CD's, Disney Dollars, sundries, periodicals, digital ad video cameras, disposable cameras, film, consumer electronics (e.g., CD players, TV's, DVD players), tobacco, alcohol, in-Park balloon vendors, Add-a-Dollar (Wildlife Conservation Fund), postage stamps, rentals (e.g., strollers,
ECV), all Titleist® and Cobra® golf equipment, National branded fragrances, treatments and cosmetics, personalization, imaging and Disney's PhotoPass® products, Lladro, Armani, Hummel, Swarovski® Crystal, Walt Disney Classics Collection, other collectibles and select merchandise. May not be combined with any other discount, offer, or promotion. Discount is for personal use only and may not be used to purchase merchandise with the intent to resell the merchandise. Not valid on previous purchase. A valid Passholder ID must be presented at time of purchase."
I would guess the fragrance at the French pavilion is either sold in a store that is considered a "Walt Disney World® Resort Operating Participant locations" or or the perfume is considered a "[n]ational branded fragrances, treatments and cosmetics" or perhaps both...