I too was curious about the legality of CEX reprinting covers. I think they got into a bit of trouble before, because when they used to reprint covers, you could only tell if you took the inlay out and looked on the underside to see a CEX logo. However, now they have a little "cover reprinted" message in the corner, on the front of the product (clearly visible to the customer).
This is why Baggie received an authentic cover with their online order, as opposed to buying in-store. If you buy online through CEX, they are not allowed to (or at least shouldn't) sell you a copy of what you purchased with a reprinted cover (as the consumer needs to be aware that is what they are buying, e.g., a game with a reprinted cover).
As for the exact legality of reprinting copyright images and logos, I'm not 100% sure on. I think, perhaps, because they are second-hand goods, some of the trading standard laws may not apply. If there was something illegal about reprinting covers for second-hand goods, I'm sure they would have been pulled up on it by now as they have been doing it for years.