Ok, the important bit about this achievement is that mali due to being unpunctual do not seem to count, at least slight ones. I got 4 points docked at the final stop, but this did not affect the achievement.
Ergo the Penalties in question are speeding, emergency brake application and braking too hard for passenger comfort. (Although the Latter is kinda hard. )
You should be on the lookout for speeding on the approach to Liverpool Lime Street as it is rather easy to speed in that 30 mph speed restriction with the strong gradient.