If an artifact or enchantment isn't destroyed (perhaps because it has indestructible or it regenerated), it won't count toward the number of +1/+1 counters put on Bane of Progress. However, if an artifact or enchantment is destroyed but doesn't go to its owner's graveyard due to a replacement effect (like the one Rest in Peace creates), it will count.

Bane of Progress's ability destroys all artifacts and enchantments, including those you control.