"It's an issue that rail companies struggle to deal with - no driver starts his day saying I'm going to drive through a red light today."
One driver, who overshot a signal by 438m after passing it at 72km/h at Papatoetoe on July 3, told company officials he was distracted by the headlight of an approaching train.
Another driver, who overshot a signal by 30.5m into a section being used for shunting, said he was distracted by a group of "rowdy youths" on the road next to Sylvia Park Station.
The third case involved an eastbound service pulling out of Kingsland Station after the train manager rang a starting gong while an "all red stop" signal was still showing.
Mr Scott would not comment on any possible disciplinary action, other than to say the company was putting considerable effort into improving staff competency.
But the report says the Transport Agency became involved in talks with Transdev after the first two incidents, and short-term remedial measures were introduced after the third.
Transdev safety and compliance general manager Huw Bridges noted last night that neither the agency nor the Transport Accident Investigation Commission had opened inquiries.
Immediate measures included written reminders to all train managers and drivers of the importance of keeping alert at all times, and the company would begin psychological screening of recruits next month.
Mr Bridges said the new electric trains had an improved electronic control system which would never allow signals to be overshot by more than five to 10 metres.
Meanwhile, Mr Scott believes a three-month trial in which some of Transdev's ticket inspectors are carrying mini-CCTV cameras on their lapels is improving train security.
There had been 36 assaults on staff since January 1 and several on passengers, among hundreds of "route crimes" including almost 80 last month. Other offending included vandalism, theft, trespassing on lines and even train "surfing" - or clinging to the outside of moving trains.
Although Transdev is still waiting for legislation to give his staff power to fine fare-evaders, Mr Scott said the cameras had enabled the issue of trespass notices against seven repeat offenders so far, barring them from trains or stations for two years. Three had been caught again on trains or at stations, and arrested by police.
Acting police inspector Graeme Porter said one was a 13-year-old girl associated with a group of troublemakers who were being investigated for a multitude of offences, including assaults and thefts.