Quantum computation promises intrinsically parallel information processing capacity by harnessing the superposition and entanglement of quantum states. However, it is still challenging to realize universal quantum computation due that the reliability and scalability are limited by unavoidable noises on qubits. Nontrivial topological properties like quantum Hall phases are found capable of offering protection, but require stringent conditions of topological band gaps and broken time-reversal symmetry. Here, we propose and experimentally demonstrate a symmetry-induced error filtering scheme, showing a more general role of geometry in protection mechanism and applications. We encode qubits in a superposition of two spatial modes on a photonic Lieb lattice. The geometric symmetry endows the system with topological properties featuring a flat band touching, leading to distinctive transmission behaviors of π-phase qubits and 0-phase qubits. The geometry exhibits a significant effect on filtering phase errors, which also enables it to monitor phase deviations in real time. The symmetry-induced error filtering can be a key element for encoding and protecting quantum states, suggesting an emerging field of symmetry-protected universal quantum computation and noisy intermediate-scale quantum technologies.