The same Girandoni Air Rifle used on that expedition was in service with the Austrian Empire before and during the Napoleonic Wars. It was difficult to manufacture and upkeep in the kind of volumes the army required, very slow to reload after a reservoir was spent, and required a lot of training.
The fragility of the rifle was a very serious problem, since many infantry battles were decided in hand-to-hand combat with bayonets. A fragile, expensive weapon had no place in such an environment. A regular musket fired often enough, was rugged and easy to make, and was very easy to use, so your average cannon-fodder line infantry kept using them.
For these reasons, the Girandoni was only really issued to small squads of elite sharpshooters and marksmen, who could sneak up on an enemy, unload their bullets in rapid succession, and then sneak away before the enemy was upon them. It was actually pretty effective at this job, and Napoleon famously decreed that any soldier captured with one of these guns should be executed as an assassin, and not afforded the dignity of a prisoner of war.
Eventually, technology such as rifled barrels, percussion caps, and breech loading made the air rifle obsolete.