The Croatian had the same 1-2 record in the group stage of the tournament as David Nalbandian but the Argentine, who lost their encounter on Tuesday, went through to the last four on sets.
"It is weird that you see the guy who you beat and he's in the semi-final," said the world number four, who lost 7-6 6-4 to Roger Federer in his final game.
"But he deserved it. He beat Andy (Roddick) in two sets and he's through.
"I cannot say that I'm frustrated," he added. "I would love to be in the semi-final. I think I played great tennis this week.
"But, you know, I'm also happy for him because he had a rough, rough year, a lot of injuries. And playing the way he was playing today, I think he deserved the semi-final."
The ATP plans to test round robin play at selected tournaments next year and, while the groups will have three rather than the four players at the Masters Cup, the potential for three-way ties will still exist.
"I'm not delighted with the project, not at all," Ljubicic said. "But, I mean, we'll see. Before you judge something, you have to test it. I'm always for testing. So let's see how it's going to go, and then hopefully here next year we're going to talk about it and see what we going to decide."