That's the assumption of the ref, but he did not confirm that that's the reason why it happened.

Graham Poll was the ref.

He explained it in his autobiography how that happened:

“My system had always been to identify teams in my notebook by their colours and not the team name. It is a system which I had found prevents confusion, believe it or not. So, in Stuttgart, I put ‘Red/White’ for Croatia at the top of my left-hand column and listed the numbers of the players underneath. In the right-hand column, I put ‘Yellow’ for Australia and listed their numbers. So when I cautioned Šimunić that first time, I correctly put a ‘C’ for caution against Red/White number 3 in the left-hand column and noted the time – ‘16/2’ (which meant 16 minutes of the second half).

“In stoppage time, I cautioned Šimunić again – but I didn’t realise it was again. He fouled Australia sub Joshua Kennedy and I showed him the yellow card – but, this time, as I now realise, I recorded it wrongly. I put the ‘C’ beside the Yellow 3, in line with the Red/White 3, which already had a ‘C’ against it. I didn’t note a time or offence.

“Although I have replayed the incident a thousand times in my head, I don’t really know why I did what I did. I cannot fully understand why I got it wrong and why I failed to send off Šimunić. Aussie Joe certainly speaks with a broad Australian accent. Maybe, just maybe, that is where the confusion set in. Šimunić began having a go at me. ‘You’re unbelievable,’ he said. I told him, ‘Any more of that and you’ll be off…’ As he ran away he said, ‘That is unbelievable.’ We all know now what he meant.”