The withdrawal of funding for students taking equivalent or lower qualifications is being blamed for queries by a number of universities about the accuracy of recent funding allocations.
Ten English institutions had their recurrent funding cut in the March allocations, and 49 others received below-inflation increases.
Two of the biggest losers - the universities of Warwick and Lancaster - questioned the funding formula, but it has emerged that several other institutions are also querying their allocations with the Higher Education Funding Council for England.
Malcolm McVicar, vice-chancellor of the University of Central Lancashire, one of the institutions concerned, said: "The methodology for calculating the cost to each university of ELQs is complex, as is the calculation of the funding for widening participation.
"We are working closely with Hefce officers to ensure that all relevant factors have been taken into account," Dr McVicar said.
In a statement, Hefce insisted that it was normal for provisional allocations to be queried, although it added that this year the withdrawal of ELQ funding was an additional contributing factor.
The Hefce statement said: "As occurs every year, institutions will contact us after (the March funding allocations) seeking further details about how their funding and student number figures have been derived.
"We have no reason to believe that more institutions have raised queries this year than in previous years.
"This year, however, there has been a new factor in the calculations relating to implementation of the Government's decision to withdraw funding for students aiming for equivalent or lower qualifications, and this has prompted some questions about the calculations and institutions' underlying data."
Final allocations will be confirmed in the summer.