Let's just get this inevitable post out of the way now...

"RRRAAAAARRGH! ME HATE FIGURE SWAPPERS AND HOPE THAT THEY ARE ALL KILLED IN AWFUL WAYS AND THAT A EUGENICS PROGRAM IS DEVELOPED THAT WILL REMOVE ALL TRACES OF THEIR GENETIC MAKEUP FROM THE HUMAN RACE!"
Seriously, though, yeah, figure swappers are jerks, and yeah, it sucks a lot to find the card of a figure you're looking for with a worthless figure in its place, but I honestly don't think it's realistic for either Hasbro or Target to be able to deal with these people. Really, let's look at what could be done:
Hasbro's side: *crickets chirping* .....really, short of packing every figure with an explosive dye pack that goes off as soon as you open it, I'm not seeing what they could do. People aren't stealing directly from Hasbro. And with the exception of the comic packs, Hasbro's packaging is pretty good at keeping figures in. Really, acting like this is Hasbro's fault is like having your car stolen and then calling the manufacturer and asking them what they're doing to find it for you.
Retail side: Okay, I know WE know a ton about joes, and that WE could tell which figures should and shouldn't be in the package, but people who DON'T collect joes just see action figures. Think about how many different figures have been released just in the 25th line (to say nothing of the ARAH and new-sculpt eras before, or other 3.75 lines like Star Wars). It's pretty unrealistic to expect someone who works at a retailer to have memorized all of those figures and how they were originally made available. We have a pretty specialized knowledge here. Hell, my wife spends hours a day in the room where I have my collection (it's also our computer room), and I know she wouldn't be able to tell me which figure was which if I pointed to two of them and asked her to name them. Why should a minimum-wage paid 16-year-old whose only interaction with joes is running them across a scanner be able to?
Now, a caveat: I DO think it's stupid when they place figure-swapped packages back on the shelf after it has been brought to their attention. There's nothing they can really do about it at that point, but they should at least throw it on the 'damaged merchandise' pile or something.
Again, figure swapping is wrong, those who participate in it are jerks, and it can be super frustrating, but I don't think pointing fingers at either Hasbro or retailers is appropriate.