Depends how long is your tibia and fibia? There's times I've put a boot on and been like woah this thing goes up to my knee wtf. But for the most part boot size relates to how the cuff is going to fit.
When you're in a boot is your calf muscle bulging way over the top of the cuff or is it flush with the back of the calf muscle.
Its really hard to diagnose the problem without seeing your legs and boots on. In all the boots I've fit over the last few years I haven't run into this problem so I'd say its rather rare and the dude that diagnosed it had to either be like 100% a boot expert or 100% lying out his ass.