If I have a 3/3 indestructible creature and i block a 3/3 then the opponent plays a spell that adds a -1/-1 counter to my creature, would the indestructible creature die because it was at 0 toughness?
No.
In the situation you describe, you’ll have a 2/2 creature with indestructible that has 3 damage marked on it. It continues to ignore the damage marked on it just like it did before the counter was placed on it because an indestructible creature can’t be destroyed by marked damage. Your opponent would need to give your creature three -1/-1 counters or otherwise reduce its toughness by 3 through non-damage means.
Remember, normal damage doesn’t reduce a creature’s toughness, no matter what Magic Arena would have you believe. The damage just stays marked on the creature until the turn ends and waits to see if the damage ever equals or exceeds the creature’s toughness.