Any soil can leach brown tannins into the water, not just composted manure.
Hopefully it was actually composted manure and not straight manure.
Did you check the smell like I advised and made sure it did not have any fowl odor?
Did it look just like rich soil, no chunks and lumps indicating that it wasn't fully composted?
There are so many different brands of composted cow manure, and a LOT are not what they say they are.
It takes common sense, a couple whiffs, and crumbling a few handfulls to determine if what you bought is up to par.
That's why I have started to use my own home made compost. Even the brand I used all the time was not consistent.
Started making compost 3 years ago, so now I have quite a bit.
Also, a thin layer of gravel doe not do the trick.
I use about an inch of gravel.
I also pack the soil down a bit before I add gravel.
If you don't pack the soil down a bit, it's too fluffy and absorbs too much water which eventually seeps out once the soil starts compacting under the water pressure and gravel weight.
Once again, common sense play a big part of potting up lilies, or any plants.
Anyway, add a bit more gravel. Leaching will not last forever. After a week or so, it should dissapate.
Do a few water changes if it really bothers you.