This is good to hear and if you do indeed fix the issue, it will go a long way toward restoring customer confidence in your products and services. That you are addressing the matter makes me much more likely to re-order from you.
Just for the record, I recently placed a fairly large order for FA flavors ( right before Christmas ) and noticed similar issues with fill levels, almost exclusively in the clear bottles with white caps for whatever reason. I did have one leak as well but it was well sealed with included shrink wrap so it must have been due to a bottle defect of some sort and I can't fault you for that. I have/had no intention of calling CS over this because I don't want or need to have the ones with the issue replaced in their entirety, I just wanted what I paid for. However it did cast a bit of pale over an order that I was anxiously awaiting which on a positive note, was received in a very timely manner.
Thanks for listening!