The problems most affect students starting university for the first time
Universities are complaining that they are having to pick up the bill for delays in students' loans and grants.
Student Finance England has apologised for a backlog of applications and says it is trying to get at least interim payments out to people.
As terms start, universities are allowing provisional enrolments and seeking only partial rents.
But they say they should not be having to cover for what they see as the incompetence of others.
The chair of the admissions practitioners group in the Academic Registrars' Council, Laura Kishore of the University of Reading, said institutions were aware of the problems some students were encountering.
She said each would be responding differently. But typically they would enrol students provisionally, provided they could show that they had actually applied for funding.
They do need to know that a student qualifies for the funding that covers tuition fees.
"If you are coming into our accommodation we are not going necessarily to ask for all your money up front," Ms Kishore said.
"Once you have enrolled, if we can use the hardship funds at our disposal then we will do that as much as we possibly can."
But she added: "We do rather feel here that we ... are being left to pick up the bill for someone else's incompetence, really."
This annoyance is shared at the Million+ group of new universities.
A spokesman said it should have come as no surprise that there would be an increase this year in applications for student places - following the trend of recent years and in light of the recession.
Student Finance England has blamed its problems on a rise of more than 16% in the number of people seeking financial support, and there being a high volume of late applications.
Its parent organisation, the Student Loans Company, said: "They acknowledge that this will be a worrying time for those students affected, and are focusing resources on making sure applications and callers are dealt with as quickly as possible."