The GTTR, which relays applications to most British training institutions, announced this week it would need to extend the deadline by three days to midnight this Sunday.
Several applicants have complained on The TES online staffroom that they did not know what had happened to their applications and feared they would miss out on places.
The GTTR has apologised for problems related to "compatability issues" with a new system.
In a message to applicants it has said that no one will be disadvantaged and it is trying to pass applications to training colleges "as soon as possible".
People who phoned the GTTR faced a long wait; a recorded message said staff would not be able to check on applications because of "essential maintenance".
One message posted on the TES website said: "I don't know how they can say that no student will be disadvantaged if people are already having interviews and being offered places."