Unfortunately, the standard operating procedure was altered during the assembly of the MSL back on Earth, and approval was not gained before the deviation to protocols was performed.
We, humans, sometimes seem to think it is ok to cut a few corners here and there, and it won't matter.
But, it does matter, especially in situations where human life is at stake, such as the space shuttle Challenger disaster in 1986 and the space shuttle Columbia disaster of 2003.
If it is not ok to launch when the temperature is too cold (and rules established to prevent such action), then it is not -- all of a sudden -- acceptable to do so, just because someone decides it is ok.
In this case concerning the drill bits inside of Curiosity, rather than having a "super-clean" environment for these drill bits, the environment was very clean, but not as clean as it was supposed to be.
It probably won't cause any problems, but the situation is not as good as would have been accomplished if 'the rules had been followed.'
Page two concludes.