The tensor network representation of many-body quantum states, given by local tensors, provides a promising numerical tool for the study of strongly correlated topological phases in two dimensions. However, the representation may be vulnerable to instabilities caused by small variations in the local tensors. For example, the topological order in the tensor network representations of the toric code ground state has been shown in Chen, Zeng, Gu, Chuang, and Wen, Phys. Rev. B 82, 165119 (2010)to be unstable if the variations break certain Z_2 symmetry of the tensor. In this work, we ask whether other types of topological orders suffer from similar kinds of instability and if so, what is the underlying physical mechanism and whether we can protect the order by enforcing certain symmetries on the tensor. We answer these questions by showing that the tensor network representations of all string-net models are indeed unstable, but the matrix product operator (MPO) symmetries of the tensors identified in Şahinoğlu, Williamson, Bultinck, Mariën, Haegeman, Schuch, and Verstraete, arXiv:1409.2150 can help to protect the order. In particular, we show that a subset of variations that break the MPO symmetries lead to instability by inducing the condensation of bosonic quasiparticles, which destroys the topological order in the wave function. Therefore such variations must be forbidden for the encoded topological order to be reliably extracted from the local tensors. On the other hand, if a tensor network based variational algorithm is used to simulate the phase transition due to boson condensation, such variation directions may prove important to access the continuous transition correctly