Luckily, the Target in my area was at least trying to be helpful with a bad situation. They were well aware of the 2 for $20 problem and notified all their cashiers to correct the price. They were also pretty annoyed at central shipping for not sending any toy box takeovers. It appears not a single Target got any, but our local Target was making good on it with discounting the price of the starter back that was pre-ordered by $20, or giving a gift card. I informed them that Toys R Us had plenty, so they we're trying to convince people to take the discount so they could buy the Takeover elsewhere. They also got a TON of Disgusts instead of Yoda. The guy in electronics was really annoyed by this, being a Star Wars fan.
Toys R Us had a ton of everything on the shelves. Every single character was accounted for and they had rows of Toy Box Takeover for sale. I'm sure they still have lots of them if others here get desperate. If I can be of help, let me know.
My actual pre-order was from Gamestop, whom didn't know about the Takeover being free with pre-order. I gave them my look, to which they rung it up and, surprise surprise, it came up free. There is no way a gaming store doesn't know about pre-orders and releases.
Anyway, my guess is that all these issues are due to there being such different release dates. More so for Takeover as the street date is messing with most PoS systems.