I used the Fire Keeper Soul through the Firelink bonfire instead of the Mute Girl in the cell.

[Zack N. Disbawls]

Did I do something wrong?

[Berengas Nº1]

yes, u need restart your game to a new one or u cant finish the game if u dont use hacks

[Fishercat]

Why can't you finish?

[Python Jones P.I.]

If you ate it you lost out on upgrading your estus flask, you can get more through NG+ but I can't see any reason why you'd need to restart.

[HALO_run]

funny i bested it on just estus flask +1 on my 1st play through

[Myrmuz [IRL]]

Using a fire keeper soul out of your inventory refills your health and gives you 5 humanity.
Using it with a fire keeper (Anastacia, Knightess, fair Lady) will increase the amount your estus heals you.
Using the Fire keeper soul you get off of Lautrec on the cell below Firelink Shrine bonfire will restore that fire keeper and your ability to use the bonfire above it. If you talk to her later on after offering Lord Souls to the Lordvessel, she will kindle her bonfire to 20 for free, which saves you a couple humanity.

You can't get back any fire keeper souls that you've used in these ways.