Problems have emerged with the marking of this year's Sats after thousands of examiners were telephoned by their supervisors to check that they were doing their sums correctly.
The Edexcel exam board, which runs the marking, sent an email earlier this month to senior key stage 2 English markers reminding them to ensure all examiners "enter the correct marks on marksheets".
But the board remained concerned that errors were still getting through, so all examiners were also phoned at the end of last week with urgent reminders to check marks.
Markers say that rules relating to recording marks - which were changed for the third year running this year and led to double-counting of some scores by examiners - are to blame.
One warned that Edexcel would have no knowledge of some mistakes already processed, meaning it could not correct them.
The controversy could add to pressure on ministers surrounding the tests, which were boycotted by thousands of schools this year, although difficulties are not on the scale of the 2008 "meltdown", when national results were published late.
Markers have had to juggle three sets of sheets in transcribing the scores pupils achieve in different elements of the writing tests on to a summary document to be sent to Edexcel.
The risk is that marks for some elements, such as the spelling test, shorter writing task and longer writing task, could be counted twice in the process.
One experienced marker said it was easy for colleagues to make mistakes. The board has also warned that a longstanding rule whereby markers have to convert the pupil's "raw" score for spelling out of 20 into an "adjusted" mark on a scale of 1 to 7, may also be confusing.
An email sent to senior markers on June 4 by an Edexcel staff member, seen by The TES, said: "As we are now checking the mark sheets received, so far we have discovered that a number of pupils have been given out-of-range marks (above the maximum allowed for that paper).
"So far, I have 43 (pupils with wrong marks) to contact markers about. While this may not seem a lot, this would not be necessary if markers made sure they were entering the correct marks on marksheets.
"Please could you (pass this on) to all markers and ask them to check their marks very carefully."
The marker said: "These mistakes could simply be put down to marker error, but they would not have happened without the stupidly complicated system which has been introduced this year."
Edexcel is not being sent pupils' scripts, so will only be aware of errors arising when a child is given a mark above 100 per cent for a particular section.
This year, for the first time, schools will not get information on each child's level until they log on to a website on July 6. Scripts without level information will be sent to schools from next Thursday.
An Edexcel spokeswoman said: "Edexcel has appropriate safeguards in place to assure marking of all exams is consistent and accurate. This was a (case of) clerical error as opposed to a marking error. As is good practice, even though the numbers were small, we wanted to ensure that clerical errors were not repeated."