See a problem description here: http://bitcointalk.org/index.php?topic=5920.0
This basically boils down to: what when you (accidentally) have a double-spending transaction in your wallet. The result is a possibly corrupted wallet, with spendings that are not accepted by the network, and change that is possibly impossible to spend as well.
Currently, this is a small problem, in the sense that it requires quite some hackery with copying wallet.dat files aroung to actually experience the problem, but as soon as import and export of wallets is implemented, it may become a much larger issue.
The patch below will detect transactions in your wallet that conflict with the block chain, and mark them rejected in the UI. They will be ignored for balance calculation and coin selection.
Pull request is here: https://github.com/bitcoin/bitcoin/pull/195