The clusters refer to when a number of schools join together to offer extended services at a larger, centrally-located school.
Alison Garnham, joint chief executive of charity Daycare Trust said there was anecdotal evidence that some extended schools were refusing to admit pupils from their cluster schools.
"We have heard from some parents that they have tried to access an extended school and been told they're part of a group of schools offering extended services, but it's often at another setting," she said. "When they approach the setting they are told the school does not take children from their particular school."
Fiona Mortlock, former head of service at after-school club provider Schoolfriendetc and now an independent consultant, backed up Garnham's views.
"The idea behind clusters is that schools group around the local high school, and it's meant to be partnership working," she said. "But what can happen is children from that school are given priority. You can also find 'good' schools don't want to take children from 'bad' schools, or the governors aren't keen on taking children from another school, feeling it may impinge on behaviour."
She added: "If a school is in an official cluster, then they should take pupils from all the schools involved."
Bernadette Ardern, consultant development manager for the north west at education charity ContinYou, said there had been some good work happening in her area around clusters of schools. "Good communication is vital," she said. "It's really important in clusters that there's partnership working from the local authority and that they do involve other partners in the cluster."
Garnham also said she had concerns over the types of activities on offer at some extended schools. "There's a question mark over whether some schools are operating as extended schools even though what they are offering is not that different from what they were already doing," she said. "There needs to be thinking around what supervised activities for children could be offered."