its more then lickly the way your foot is sitting in the boot.
Did you get a footbed when you got the boots fitted. If not this should be your first thing to do.
If your foot prontaes in the boot, even if its been heat molded, there will be pressure on the inner ankle from the shell.
Now some bootfitters may just stretch the shell on the inside, and this may help sometimes but its not getting rid of the problem so it wont defiantly help.
If you get a footbed which keeps your foot in a more neutral position if you then need a shell stretch you know it will work as you have controlled the foot first.
Usually I will make a footbed then if they need a slight stretch I will do that for free.
In my opinion Sidas make the best custom footbeds. Expect to pay $150-200