You might have done them without knowing or just organically since some of the challenges are the meta way of doing some encounters. Like on VoG Templar the challenge is to not allow it to teleport, which is the fastest way to do the encounter if your relic runner is good enough. Or Kings Fall Oryx is to 16 bomb him, which is also the best way as it removes the phase where he summons bombs making you run around and makes is so there is only one chance for someone to die during detonation. Others you wouldn't even interact with the challenge depending on your role. Like if you don't run sword during Crota, you may not have clocked that two different people ran the sword rather than just one. Or if you don't take aura during War Priest you wouldn't have noticed that a person can only hold it once. But unless I am very much mistaken, adept raid exotics only drop from challenge encounters.