I think this is due to them adding refundability and breakfast being included, which the hotel sites don't bundle in to the room type. They also have "assigned on arrival" types, which I've never used as they're often more expensive than the cheapest room type, which is what I would expect them to assign to me.
The site also seems to use a lot of other intermediary sites to book the hotel, I've heard some weird names such as 'DBO Holidays' when checking in, which may add a different point where the type/amenities could break.
The only time I've had an issue is with 2 reservations at one hotel, where I booked the cheapest rate on AAH, which happened to be a room for 3 people, however the room I was assigned was only for 1 person. It wasn't an issue since I was traveling solo (and had indicated as such on the site to avoid the per-person taxes that would have applied), so I never complained, but it's definitely not an issue with just amenities.
To your point about bundled rates to include breakfast, I've had it display rates with and without breakfast (with commensurate difference in prices) for hotels like Embassy Suites or Hampton Inn or Holiday Inn Express, where BREAKFAST IS FREE FOR EVERYONE. So definitely people need to pay attention to the GIANT set of choices when they book...seems like they show only 5 options at a time, and you can click more to see more. It's a mind boggling number of choices, but it's made me feel like I can see more of what the local hotel room types really are, compared to just booking a random Marriott/Hyatt/Hilton corporate website reservation. It's a lot of detail in the room types/descriptions sometimes.