We consider error correction, based on the theory of non-commutative graphs, for a model of a qubit interacting with quantum oscillator. The dynamics of the composite system is governed by the Schr"odinger equation which generates positive operator-valued measure (POVM) for the system dynamics. We construct a quantum channel generating the non-commutative graph as a linear envelope of the POVM. The idea is based on applying a generalized version of a quantum channel using the apparatus of von Neumann algebras. The results are analyzes for a non-commutative graph generated by a qubit interacting with quantum oscillator. For this model the quantum anticlique which determines the error correcting subspace has an explicit expression.