Usually a distributor will look for an exclusive deal for the territory they operate in (and not just in gaming-related businesses), or as close to exclusive as they can get - involving, say, discounts for them, but not for others who manage to get a tow in the door. Which was presumably all fine and dandy before someone invented teh internetz, and in the case of M:tG, I presume suddenly saw drops in sales as ppl started buying online in cheaper territories rather than via the retailers they they supplied. So presumably they went to WotC and cried foul. So WotC went to Amazon (or the US distributor went to Amazon.com and the UK one went to Amazon.co.uk) and said "Stop that or we won't sell to you anymore..."
I could be way off the mark, of course... this is mostly conjecture.
I had a similar problem recently, I had a basket of around 12 items from amazon, due to having one of those days where you wake up and say "fuck saving, I'm bored." But, the buggers wouldn't ship half the items to ireland, pooper games mostly and a wireless keyboard/mouse set.