Not only were the Trapdoors single shots, but the Spaniards filled the clouds of BP smoke with bullets.  Not sporting.

But the Army had a long history of preparing to fight the last war.  When looking for a smokeless powder rifle, they did not really think about fighting a European military force in a protracted (?) ground war.  The minds of those making decisions were set on the Indian Wars type of fighting, a series of small quick fights for which the Krag would have been ideal.