Pupils' answer books, which were separated page-by-page to be scanned by computer for marking on-screen, were posted to examiners after being put together again when the trial was revised last month.
Around half of one examiner's allocation of several hundred scripts were re-stapled in this way. In some cases the staple made it hard for a marker to read part of the top of the script.
Several answer books were stapled so badly that up to half of the 12 pages were not attached to the rest of the student's work.
The examiner said: "This is a recipe for disaster for a candidate. These pages could go missing."
As The TES reported last week, the Edexcel board decided to scale down its trial of on-screen GCSE, marking, re-allocating around 100,000 papers for traditional marking. About one million papers have been marked electronically.
Edexcel has denied that computer problems were to blame. But The TES has seen three emails from the board alerting markers to "performance issues" and "technical difficulties" with the system, known as ePen.
Two examiners said ePen had repeatedly been unavailable to them. One claimed it had taken around 10 hours to get through a sample of 15 scripts on-line, which would normally have taken at most four. The changes cost examiners a week of marking time, it was claimed.
Examiners are also unhappy about being offered only pound;100 in compensation by the board, after signing contracts which state that the work will be conducted on-screen.
An Edexcel spokeswoman said the board had faced some "technical challenges" with the trial, but overall this had been a "massive achievement", with more than one million papers marked electronically across many subjects.
She denied that the stapling had been rushed, saying that all papers were stapled together after scanning electronically.
The issue will heighten controversy surrounding Edexcel, which became the first privatised exam board last year. The news comes as it emerged that it is running a call centre in Malaysia to handle aspects of the exam process.
Around 30 staff in Kuala Lumpur, and 50 in the UK, have been employed to ring examiners after they have completed marking, asking them what score they have given each candidate.
The spokeswoman said the system helped the board speed up the processing of results. She would not say how much the Malaysian staff were paid, but said it was "a good rate for the region".