Hundreds of teachers may have been wrongly informed by their heads that they could leave their applications beyond Monday's deadline, the second largest teaching union claims.
And this was just one case of misinformation in schools, says the National Association of Schoolmasters Union of Women Teachers.
Thousands of teachers wrongly told to prepare portfolios of work to accompany applications.
Heads refusing to process the applications of people who work in more than one school.
Staff in special measures schools wrongly being told they could not apply.
Staff older than 50 being told they were not eligible.
In addition, the union has heard of heads wrongly preparing to delegate assessment to their deputies, and several heads misguidedly arranging to meet in groups to moderate applications.
It also claims that newly-qualified assessors are unofficially touting for business advising schools on dealing with the process, while five local authorities were threatening to take teacher contracts away from advisory staff if they applied to cross the threshold.
One Sheffield head allgedly told a husband-and-wife team that only one application per family was allowed.
Nigel de Gruchy, NASUWT general secretary, described the problems as "predictable".
He said: "The whole thing has effectively had to be cascaded down from the Department for Education and Employment to local authorities through to 25,000 heads in the space of a few weeks.
"I would hope that most of these problems will be sorted out by Monday and won't fatally undermine applications.
"But if there have been serious problems with the applications deadline, it would be a huge issue and the Government would have to look seriously at extending the deadline."
However, Esther Williams, senior assistant general secretary at the National Association of Head Teachers, said: "All our headteachers have been alerted on several occasions that the deadline is June 5 and we are not aware of any heads who were not clear about that."
The problems come after training for headteachers assessing teachers for performance-related pay was changed at the last minute after heads bombarded The TES with complaints.
A Department for Education and Employment spokesman said: "The deadline for applications is June 5 and we have said that all along.
"We are very surprised at the misinformation reported by the NASUWT. Every point they raise is clearly addressed in materials sent to all schools and LEAs on March 24."