Well, science is expensive. Even more so if you want to combine it with a metric buttload of technology transfer.
Honestly, going wildly over budget is pretty much par for the course in any sort of large scale infrastructure project in Europe. With the way tender procedure’s work in the EU, it’s entirely expected that things are going to end up being more expensive and take twice as long. It’s stupid and wasteful, but it’s “public money” and not going to change any time soon.
ITER isn’t a EU but international project and was never meant to be cheap: If you want something to be cheap you don’t ask ten different companies in ten different countries to produce one coil each.
Doing it that way was a political decision, it’s about technology transfer, building knowledge in different countries, not building a cost-efficient reactor.
You can build more complex stuff much cheaper, e.g. the Wendelstein 7x project costs 1.3bn, and that’s including all wages for the general Max Plank outpost in Greifswald for 18 years. The reactor itself did cost 370m. It’s way smaller than ITER, yes, but have a look at the Lovecraftian geometry and you see why it’s just a tad harder to build.
It’s not an EU project, but there are EU countries involved in the funding, which means EU tender regulations apply.
Wendelstein is cheaper, but according to wikipedia it also went over budget. “[…] while the total cost for the IPP site in Greifswald including investment plus operating costs (personnel and material resources) amounted to €1.06 billion for that 18-year period. This exceeded the original budget estimate, mainly because the initial development phase was longer than expected, doubling the personnel costs.” (The original source is a dead link, but you could probably find something corroborating fairly easily.)
I’m not saying ITER is a bad project, I don’t even think the cost is a problem, I just think that the regulations surrounding the financing of these kinds of projects often do more harm than good.