Lethal damage, damage from a source with deathtouch, and effects that say “destroy” won’t cause a permanent with indestructible to be put into the graveyard. However, a permanent with indestructible can be put into the graveyard for a number of reasons. The most likely reasons are if it’s sacrificed, if it’s legendary and another legendary permanent with the same name is controlled by the same player, if it’s a planeswalker and another planeswalker with the same subtype is controlled by the same player, if it’s a creature with toughness 0 or less, or if it’s an Aura that’s either unattached or attached to something illegal.