I don't think the spending is really a problem, but possibly the many work-hours of brilliant minds that might be more fruitfully employed working on different problems.

Let's not pick on the LHC for that. How many gobsmackingly brilliant engineer-hours have gone into optimizing ad targeting or fine-tuning purchase attribution?

Not to mention, the LHC is responsible for a lot of innovation in it's own right, just in terms of hardware, software, etc.

The bigger picture is that only so many resources are going to be devoted to researching fundamental physics (both money and hours of work from human beings). If the majority of those resources are focused on a dead-end theory, then the opportunity cost is quite literally everything else.