Are you certain they're counting towards your minutes?
If they're Facetime, they go through Facetime, Apple's service, unless you have Facetime set to call you on your cellular number (I don't know how Facetime works).
There IS a bug that's been in T-Mobile's system that says all your minutes are used if you're prepaid. I don't know if it's been fixed yet, but if it hasn't been fixed, that would be why you would be seeing all your minutes used.