I've got/had tons of records that do this...
Fact is that record pressing has gone downhill from how it was thirty or forty years ago, something to do with the expertise of cutting masters on the lathe not being so widespread, and most of the vinyl used nowdays is quite thin and made up of mostly lower grade recycled vinyl. You can really see the difference if you go and grab an old record form the 60's or summat, then compare it up to the 12" you just bought. More than likely the 12" you just bough is much thinner and much much more bendy than the old one, which means that things like this happen way more often....
Just take it back to the shop, tell them it's a mis-press and can you have another? - any good record shop will swap it without question, as they probably know the above. If they haven't got another copy then they should offer you a couple of quid off the price - which is great news if the affected side is the a not so great b-side that you didn't want anyway.
You shouldn't really keep your records stacked on top of each other, but as long as your piles aren't too big, and are kept reasonably square you shouldn't really cause any real harm, as long as their not too close to a radiator or something!
My dad had every single release by the rolling stones ever, then left 'em on the back seat of his car and went to the pub when he was young... The sun warped every single one of them, all completely ruined - they looked like flower pots by the time he came out the pub...