The Walmart promo is intentional, so buy those with confidence (unless you don't like their ecommerce setup, which is totally fair). Amazon has price-matched many of those $50 games, those should be fine to buy as well. All glitches from earlier this week seem to be fixed, so the best you can expect going forward for anything Walmart doesn't put on sale for $50 are the blanket 20% promos at Amazon and Best Buy.
I don't think anyone's reported earlier orders getting their discounts fixed, so so far so good. Amazon's are likely to stick. Others may not, but we'll see when ARMS ships.