So i examined the bags close for the mines of moria. wow, first time I've seen this done which is how i missed it. They took Jabba and the Gamorrean Guard but not the others. Whoever stole the minifigs resealed the bags with a heat device which melted the packaging back together so that it was impossible to tell they had been opened unless looking super super close.
You have my deepest sympathies because this is exactly what happened to me with my Jabba's Palace set. The bags were opened and very carefully resealed, but on close inspection do not match the seals on other bags. It seems sets with bigfigures are the most common targets for this type of abuse because they fetch good money on ebay or bricklink.
I wish someone would catch the evil fuck(s) who think they can get away with it. Amazon has no system for tracking this sort of abuse, I know because I tried to file a complaint about it. You would hope they'd have a system for matching complaints about missing items inside boxes to people who have returned items to amazon that subsequently end up on amazonwarehousedeals... but they don't. At least not yet.
I understand mistakes COULD happen, but if someone is returning tons of LEGO sets that should be a very clear red flag. I'm also not ruling out that amazon employees themselves could be the culprits, because they have to inspect returned or damaged items before they can be sold on warehousedeals. The perfect access for a minifigure thief.
I learned the hard way, but LEGO fans need to be very aware on this: If you purchase a set from amazon warehouse or from any other seller where you even mildly suspect that the box may have been opened... please do yourself a favor, and examine the contents for missing minifigs PRONTO.
You have lots of options, but it's better to react quickly especially if it's an older set, because LEGO may no be able to provide minifig replacements for some OOP stuff.
Finally, I just want to say that I feel amazon warehousedeals is a great resource for bargain hunters, but it's not without its pitfalls. Buy wisely. If the set contains rare or unusual minfigs (like bigfigs or figs with special heads), know what you are getting into. If it's a creator set or something like that? It's probably a safe bet.