Apollo 11 (which included actually landing on the Moon for the first time in human history!) cost only $355 million* in 1969. That's a little over 3 billion in 2025 dollars. How has a comperatively "simple" flyby become so expensive?

You could also look at the same ISS mission with another contractor: Boeing got paid twice as much and then failed to bring the astronauts back in Starliner. So obviously NASA is overpaying some contractors, but that's probably only part of the story of where all that money is going. For 90 billion NASA would have delivered multiple Moon landings in the 70s - with inferior tech at that, and having to figure it all out for the first time. Don't underestimate how difficult it was.

* https://www.sciencedirect.com/science/article/pii/S026596462...

You should compare against Apollo 9, which was 96% as expensive as 11 and much closer in mission profile. Then you don't need to worry about comparisons on simple flyby vs full landing