We present a systematic investigation of muon-stopping states in superconductors that reportedly exhibit spontaneous magnetic fields below their transition temperatures due to time-reversal symmetry breaking. These materials include elemental rhenium, several intermetallic systems and Sr$_2$RuO$_4$. We demonstrate that the presence of the muon leads to only a limited and relatively localized perturbation to the local crystal structure, while any small changes to the electronic structure occur several electron volts below the Fermi energy leading to only minimal changes in the charge density on ions close to the muon. Our results imply that the muon-induced perturbation alone is unlikely to lead to the observed spontaneous fields in these materials, whose origin is more likely intrinsic to the time-reversal symmetry broken superconducting state.