Analyzing the phenomenon of deconfinement from a holographic point of view, it appears that the brane configuration in the bulk, corresponding to the confinement phase imposes a restriction on the strength of the holographic quantum error correction procedure. This restriction is partially removed when the transition to a deconfined phase occurs. The brane configurations corresponding to the bulk instantons are analyzed and it is shown that they cannot reach the region of the bulk that would ensure maximal error protection in the confinement phase, while keeping non-zero instanton size. In the deconfinement phase on the other side, we have a configuration that allows a higher degree of quantum error protection, still preventing the maximal protection allowed by the holographic principle. This suggests that the strength of quantum error correction codes in QCD systems is fundamentally limited both in confinement and deconfinement phases.