I’m gonna guess you used it on breach gear. Some of those had enchants that are no longer valid, so the resulting essence can be restricted to different gear than what you pulled it from. I wasted a few essence embers this way as well. I basically sold off my gear stash to make sure it wouldn’t happen again. If you have a lot of old gear, I suggest checking Full List of Enchantments - Google Drive to make sure what you are trying to do is valid. Alternatively, you can use Build Planner – No Rest For The Wicked Tools to plan out a valid build before using your embers.
As far as drop rates, I also have 500 hours in the game, though definitely not entirely in the together update. I’ve got four builds fully fleshed out with plenty of mistakes along the way. The drop rate is definitely not the greatest, but there are ways to optimize your time. A Guide To Embers and Exalting So You Don't Waste Them