This is the full-on electrical engineer explanation, just because.  So forgive me if it's too abstruse.

These circuits work by chopping the voltage from the battery, and depending on the motor to average the voltage out to make a somewhat steady current.  So when you're running at 50% throttle, the motor doesn't see 12V -- it sees 24V alternating very rapidly with 0V.  The motor has a property called inductance, which means that it more or less acts as if it's just seeing a steady 12V.

However, it doesn't quite smooth out the 24V entirely -- there's a phenomenon called "ripple current" caused by the motor inductance not smoothing things completely.  There's also a phenomenon called "eddy current", that happens no matter what.  Both of these will tend to use cause the motor itself to heat up.

But, unless the problem is extreme, you're probably OK.