Not sure which app exactly you are using, but most flight tracking sites and apps use ADS-B and MLAT to determine a plane’s position (and more).
Both require the aircraft to be equipped with a suitable transponder.
A lot of GA aircraft are not equipped with one and are thus completely invisible on such sites. Even some airliners may or may not be equipped (depends where). Military aircraft may be equipped or not, and may turn it on or off depending on the mission, or even during different parts of the mission. Other specific aircraft (like emergency services, firefighting aircraft…) also may or may not be equipped.
So a plane could very well be in the air and not show up on those apps and sites.
On the other hand, in some airports you may be able to see some ground vehicles which will never get off the ground shown on the maps, because they are equipped.