effects that say "-3/-3" aren't the same as damage. It's a reduction in power and toughness. When a creature has toughness equal to zero or less, it's put into the graveyard. This is not a "Destroy" effect and is not damage. The effect, commonly referred to as "debuff" completely ignores indestructible.

There was no glitch, only a rule you were unaware of. I encourage you to become familiar with the rules of the game rather than file a report on a glitch that doesn't exist.

Locthwain Scorn does not deal any damage, so there is no damage, lethal or otherwise, in the first place. The state based action that destroyed lethally damaged creatures doesn't apply. The one I cited does. The state based actions indestructible helps against are the following ones (note the very important condition they begin with):

704.5g If a creature has toughness greater than 0, it has damage marked on it, and the total damage
marked on it is greater than or equal to its toughness, that creature has been dealt lethal damage
and is destroyed. Regeneration can replace this event.

704.5h If a creature has toughness greater than 0, and it’s been dealt damage by a source with
deathtouch since the last time state-based actions were checked, that creature is destroyed.
Regeneration can replace this event.

With your creature having 0 or less toughness, neither state based action applies. The one I cited already , does:

704.5f If a creature has toughness 0 or less, it’s put into its owner’s graveyard. Regeneration can’t
replace this event.

Dying for having 0 or less toughness is not destruction. Indestructible doesn't mean unkillable, it only means "cannot be destroyed".

704.5f If a creature has toughness 0 or less, it’s put into its owner’s graveyard. Regeneration can’t
replace this event.