This Coindesk article says that:
“So as transactions are being created, malformed/parallel transactions are also being created so as to create a fog of confusion over the entire network, which then affects almost every single implementation out there,” he added.
Antonopoulos went on to say that Blockchain.info’s implementation is not affected, but some exchanges have been affected – their internal accounting systems are gradually going out of sync with the network.
How does this getting out of sync occur? Here's my understanding; as a transaction is created, malicious users create hundreds of transactions in the network that are identical except for a mutated signature. The original transaction may or may not be confirmed because a mutated version may get confirmed in the blockchain first.
For example, Mt. Gox, which used an automated system to approve withdrawals (as the article states), would consider a withdrawal transaction approved before it was actually confirmed in the blockchain. Once a mutated version of that transaction was confirmed in the blockchain, Mt. Gox's accounting system had a problem because a transaction it assumed was confirmed (and therefore had already "lost" the Bitcoins for) wasn't actually confirmed.
Is my understanding correct?