During America's Civil War, why were so many amputations conducted?

Because infection was still a very serious issue that claimed more lives than actual combat. The only way to fight serious infections from wounds at that time was to remove the wounded limb to keep the infection from spreading.

Really, it all comes down to the more primitive level of medical science they had in those days.

Also, when a projectile like a bullet ripped through flesh and bone causing traumatic damage, given the degree of surgical skill, often the only recourse was amputation .