Things such as a needless biopsy of healthy tissue, leading to an infection and sepsis.

A colonoscopy perforating the bowel and leading to an infection and sepsis.

These things happen, they are not common but they are not zero-chance events either.

And you have to consider the opportunity costs of consuming the doctor's time, the labwork, and the facilities, possibly delaying treatment for someone else who actually needs it.

Yes it would be better if it took these into account but doing so would not change the overall numbers.

Risk of perforation is something like .03% and almost never fatal whereas a colonoscopy reduces colorectal cancer mortality by 60-70%.

>And you have to consider the opportunity costs of consuming the doctor's time, the labwork, and the facilities, possibly delaying treatment for someone else who actually needs it.

That is also rarely true. More often, greater demand for a service soon yields economies of scale, more efficiencies and overall more patients served at a lower price. Low volume is expensive, high volume is cheap.