One thing she was definitely talking about was Dormammu. You could even say she was literally talking about that specific incident, where the stone is used as a weapon in order to bring Dormammu to heel when there were basically no other options. But she could also mean other things as well.
But while Earth-199999 doesn't have the Time Stone anymore
, they DO have Dr. Strange who is meant to be the greatest Sorcerer Supreme in history, in any reality.
One order of business for the next Dr. Strange movie may well be addressing the problem of not having any universe altering artifacts
on hand in case some shit goes down, and Strange finding a solution for that.