I'm confused, which warning lights came on when? Rear amber or red warning, or front amber or red warning?
It sounds like neither warning was on at the BMW check, so they just went by thickness measurement. To be honest it is doubtful that the pads need replacing until the red warning comes on, so not sure they can be criticised. I get more annoyed when they say they need changing and there is clearly 4+mm of life left.