Creating opportunities for meaningful social relationships between students with and without special educational needs (SEN) through collaborative learning has been suggested as a way to facilitate all students’ social inclusion in classroom activities. However, little attention has been given to the peer interaction processes leading to unsuccessful knowledge co-creation in mixed-ability peer groups including students with and without SEN. This study addressed this research gap by conducting detailed observational analyses of the social exclusion during group work of students with and without SEN, and how the students with SEN responded to their positioning as unequal learning partners. The results were based on video-recordings of 24 lessons involving fifth graders in Finnish school spaces featuring open and flexible learning environments. The data were analysed by applying multimodal conversation analysis. The results showed that although the students with SEN performed relevant on-task initiations and contributed actively to the ongoing group work, their contributions were misaligned by ignoring, denying, invalidating their contributions, manipulating shared learning materials, or downgrading their status as help givers. Despite this, students with SEN continued to orient toward collaborative working by persistently initiating joint activities, negotiating their task performance and struggling to ensure their right to contribute. The study underlines the importance of instructing all students to create a warm and attentive learning community in which every member of the group has equal rights to participate and to be recognised as a full member of the learning community.