It never saved your 3oC, it just keeps your checkpoint so you can do it again. They patched 3oC being useful immediately, now there is a 6 minute cool down (but you can still pop them right away). So when you kill a boss and it takes the 3oC buff, look at your clock and don't pop another until it has been 6 mintues.
This isn't actually correct. People still don't know what the diminished drop cool down rate is, but using coins immediately after consuming one (killing an Ultra) is highly recommended if you have the coins. It still has a chance to drop an exotic.
For instance, after the patch I would kill 1 shield brother and he would drop an exotic. I would then pop another 3 of coins and kill the other brother and occasionally get an exotic. Or vice versa, 3oC consumed via first brother and no exotic drop, so I pop another and end up with an exotic.
Same with Regicide, with the taken ogre and colossus ultras. Those can back to back. Any ultra can, it's just a reduced chance. But 3oC come easy generally, so stock up and ALWAYS have one popped.
Same with the Shade of Oryx in the raid and Oryx himself. Both can drop exotics and it has happened multiple times. Generally Oryx is dead within 5-6 minutes of the shade kill, but can still drop the engram with a 3oC. Or if you have to do 2 shades, then Oryx, it's 3 chances.
There was a really good guide on reddit, but it's buried under 10000 idiot 3oC posts.
TLDR; If you have plenty, use 3oC on every ultra/always have one active. If you are low, use them after 6 minutes after killing an ultra and rolling for an exotic. Never use more than 1 at a time.
Bungie should just put in a cooldown timer, but it's not a big deal.