I echo deelmakur's comments that while not a big deal on a case-by-case basis, this is likely widespread and going unnoticed. And it goes beyond CPs and companions as evidenced in the 'used miles to upgrade, but they deducted e-upgrades anyway'.
Almost have to wonder, with other things, if this is something they arent in a hurry to fix because it benefits them.
Keep an eye on those upgrade accounts!