The problem was one of several revealed by an investigation into marks given to GCSE religious studies pupils from West Park school, in Derby.
The independent Examinations Appeals Board (EAB) this week rejected an appeal by the school, which wanted the company to re-mark the scripts of all 1,800 pupils in England who sat the board's Christianity paper.
The watchdog said there was insufficient evidence of a "global misapplication" of marks despite problems with the school's results, but have demanded that Edexcel go back over a wider range of scripts.
West Park first requested that all 325 of its Christianity papers be re-marked last year after pupils peformed significantly differently from expectations.
The school was not satisfied when a principal examiner re-marked only nine and accused him of making additional errors. But the exam board rejected its demands to re-mark further papers.
However, after the school appealed to the EAB, Edexcel's chief examiner re-marked all West Park's papers and increased the marks of 60 per cent, some by as many as 15 points.
The school complained that scores given to several students' answers seemed to vary dramatically between markers. An answer by one candidate was given two marks by the assistant examiner, four by the principal examiner and then eight - the highest possible score - by the chief examiner.
Confusion was exacerbated by the fact that all the scripts were originally marked on-screen and the electronic ticks were not recorded, although the point scores were.
The EAB ordered Edexcel to improve the training for its senior staff in re-marking and to create "a clear audit trail for online marking to enable the work of assistant examiners to be more effectively monitored".
Edexcel said this week that its on-screen marking system would be central to a pilot scheme this summer when GCSE students will see their grades and marked scripts online.
An Edexcel spokeswoman said it was pleased with the board's ruling and would be discussing its recommendations with senior examiners later this month.