The problem was not knowing about breechloaders. There had already been trials: the Hall rifle was produced at Harper's Ferry in the 1830's, the Navy had tried the Jenks in the 1840's ( though, mostly because of political pressure). In the 1850's, the attitude of the War Dept. was, yes, the future is breechloaders, but we're not there, yet.

The problem very much was production. There were about 275,000 Springfield Model 1842 muskets, 60,000 model 1855 rifled muskets, and around 1 million Model 1861 rifled muskets produced in all, but those weren't enough. During the War, the War Dept. had to buy not only around 670,000 new Springfield rifled muskets, but import more than 420,000 Enfield rifles from England and hundreds of thousands from Austria, France, Germany. There was simply no way to re-equip every soldier with a completely different gun.

Breechloaders were also more complex to make. Armory practice was centered around interchangeable parts, and that requirement for uniformity of manufacture meant many more steps in manufacturing. That in turn required more machines, jigs, fixtures, gauges, etc. It was a very great step above what was required for an armory to make muzzleloaders. That step was the biggest reason for the War Dept. selecting a breechloader after the War that was a compromise design: the head armorer at Springfield, Erskine Allin, figured out a way to convert the 1861 Rifled Musket. Cutting that corner promised to save an enormous amount of work by not having to make a different stock, barrek, furniture and most of the lock. Though the work to modify and improve the Allin Conversion into the Trapdoor Springfield was, after twenty years of modifications, more than would have been needed for a completely different gun, it's easy to understand the decision: more than a million existing guns would have otherwise been junked. .

The War Dept did try to supply breechloaders to the troops most in need. It is very hard to deal with a muzzleloader while sitting on a horse, and the greatest need therefore was the cavalry. . Hundreds of thousands of carbines were bought , of various kinds: Sharps, Smith, Gallagher, Burnside, Joslyn, Gibbs, Starr, Spencer, Maynard....And militia infantry units sometimes would supply themselves with more than muzzleloaders: a couple of Pennsylvania units equipped with Henry rifles made the Battle of Franklin even more costly for John Bell Hood. So, breechloaders were used during the War. Just not by everyone.

TL:DR Muzzleloaders were used because they couldn't make enough breechloaders to replace them.

First of all, your premise is a bit flawed. In 1860, the only Great Power that had a breech-loading infantry rifle was Prussia. While the Austro-Prussian War of 1866 would show just how decisive the firepower advantage offered by a breech loading rifle was, the Dreyse and similar early breech-loading designs had numerous issues that would leave armies reluctant to adopt them. It wasn't until the second half of the 1860s that other Great Powers started to adopt breech-loading infantry rifles, itself in reaction to lessons of the American Civil War and Austro-Prussian War.

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The US Army in the Civil War had several issues that compounded on the existing issues with breech-loading rifles. Probably most significant was the rapid expansion of the US Army when the war broke out. When war broke out in April 1861, the regular US Army consisted of just 16,000 men. The Army's budget was fairly low and its focus was on being a frontier force, so the adoption of cutting-edge and unproven weapons wasn't a priority for the Army. The Army ballooned rapidly when war broke out - a half million Northern volunteers responded to the first call right after the outbreak of war - and this rapid expansion left the Army struggling to meet demands for equipment. US arsenals were spun up at full capacity to produce the muzzle-loading patterns of rifle they already had in production, and foreign designs like the Pattern 53 Enfield and Lorenz rifle were procured to meet demands. In such an environment, making the switch to a breech-loading design wasn't feasible - the Army lacked the time and money to deal with the trials process, re-tool factories, and retrain units during wartime.

A less obvious issue was logistics. The Civil War was fought over a huge area with far less infrastructure than the armies of the Great Powers in Europe were able to rely on. Ammunition supply was a very real concern for armies, and the increased fire rate of a breech-loading rifle (or even worse, a repeater) presented the threat of running out an army's ammunition faster than they could replace it. For designs like the Henry lever-action, which used metallic cartridges, ammunition supply was even more of an issue because the army wouldn't be able to procure ammunition in the field like they could with the paper catridges of their normal rifles. Apart from ammunition, the more complicated nature of a breech-loader also required a supply chain of spare parts (the Dreyse, for example, needed a steady supply of firing pins and obturator rings).

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All that being said, the advantage offered by a breech-loader was recognized by the US Army during the war. Grant's Virginia campaign in particular showed that, in the right circumstances, logistics of the time could keep up with the armies, and the later battles in the war had come to show just how important volume of fire had become. Once the war ended, the Army was finally able to work on procuring a modern breech-loader. However, Congress wanted to demobilize, so budgets were slashed and procurement came with the stipulation that the new rifle must be a conversion of existing stocks. That put a premium on a cheap conversion, resulting in what became the Trapdoor Springfield.