Judge Bruce Davidson said the company knew of the door hazard for several years.
He said the accidents happened despite "remedial action" the company and wider industry took to address concerns about door safety.
"Until mid-2013 there was little maintenance or checking of the doors of the bus fleet."
The judge said some passenger complaints may have been directed to agencies instead of the company directly.
He said all people caught in doors were "frightened, scared and worried" about the incidents.
Judge Davidson said parent company NZ Bus had put in "significant and costly" measures to improve the Wellington firm's safety processes since buying the company a decade ago.
Judge Davidson said culpability was the key issue in understanding the case.
The prosecution argued the firm had a high level of culpability and the penalty should be a $100,000 fine.
Judge Davidson said mitigating factors included the company's guilty plea, a new company safety plan, and other new safety measures.
The key safety measures related to "improved driver visibility" achieved through new door sensors, better positioning of mirrors, and the installation of CCTV cameras.
Defence lawyer Adrian Olney suggested a fine with a starting point as low as $20,000, and said the company had been responsible and co-operative in resolving the door safety issue.
"I'm left with an overwhelming sense ... that this is a risk that can never be eliminated but one which can only be addressed by mitigation."
Judge Davidson said the starting point for the fine was $35,000.
He considered a 15 per cent discount for mitigating factors including the company's remedial steps and its co-operation with authorities investigating the incidents.
The early guilty plea reduced the penalty further, to around $22,500.
The charge carried a maximum fine of $250,000.