The PNR cowtool only looks at the first ticket for each passenger to determine the cost.

When you have multiple tickets on the PNR, it's going to be wrong. There is likely enough data to show this entirely properly, there just hasn't been enough demand for the effort. I think you're the second or third person who's run into this in 4 years.

As D582 said, this will almost certainly post correctly (or at least as correctly as any flight does), and I would not spend any time worrying about it unless/until it doesn't.