There shouldn't be such transactions, there can be fault at merchant end accepting double-spend transaction during fork time.
When the fork was first being looked into, at March 12 2013 and at 00:03 AM the main net at the time (mined by v0.8 clients) was at block 225439, yet other clients were stuck on the fork at the time (mined by v0.7 and prior clients) was at 225431.
00:00 sipa ;;bc,blocks
00:00 gribble 225431
00:01 sipa but it seems blockexplorer is stuck too...
00:01 sipa as i'm on 225439
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http://bitcoinstats.com/irc/bitcoin-dev/logs/2013/03/12So even before anyone knew for sure that a fork was underway, there could have been transactions with six confirmations on the v0.8 side. If for whatever reason those transactions didn't also already get included in blocks on the v0.7 side, there was the opportunity to perform a race attack to double spend the transaction that had already been included on the v0.8 side.
We now know that exact scenario is what happened with the transfer to OKPay that is being claimed to have been successfully double spent. Though in that instance, it was after the alert went out that OKPay still processed the deposit as being valid. So that specific incident could have been prevented had they halted processing once the alert went out, but there still was a window between when confirmations would occur since the fork started and when the alert eventually went out.