A principal moderator's annual report on statistics said very few students had been encouraged to choose their own investigation topics, which limited their scope to demonstrate independent work.
It said: "Too much guidance is still preventing the best candidates from producing work commensurate with their considerable ability."
The findings came in the examiners' reports from the Edexcel board, which also praised many teachers for helping pupils do well.
But in the Shakespeare English GCSE paper, examiners criticised "an over reliance on teacher notes and a tendency to similar phrasing and the use of the same quotations".
Reports for French, applied French, German and Spanish said many pupils had been over- prepared in their orals. In the worst case, all of one school's pupils replied with identical answers.
In French, a significant minority of teachers worked through set questions, denying higher-ability pupils the chance to gain points.
For double science, some schools and colleges got their top pupils to carry out investigations aimed at the foundation tier, again limiting their potential grades.
In one history paper, many pupils appeared to have missed an essay question due to a confusingly placed blank page. Nine per cent of entrants failed to answer this question, which was unlikely to have been because they ran out of time.
The board warned teachers to better prepare students. Heather Scott, of the Historical Association, called for a paper redesign.
GCSE results, pages 3 and 13