We performed ab initio valence-space in-medium similarity renormalization group (VS-IMSRG) calculations based on chiral two-nucleon and three-nucleon interactions to investigate the anomalous seniority breaking in the neutron number $N=50$ isotones: $^{92}$Mo, $^{94}$Ru, $^{96}$Pd, and $^{98}$Cd. Our calculations well reproduced the measured low-lying spectra and electromagnetic E2 transitions in these nuclei, supporting partial seniority conservation in the first $\pi g_{9/2}$ shell. Recent experiments have revealed that, compared to the symmetric patterns predicted under the conserved seniority symmetry, the $4_1^{+}\to 2_1^{+}$ E2 transition strength in $^{94}$Ru is significantly enhanced and that in $^{96}$Pd is suppressed. In contrast, the $6_1^{+}\to 4_1^{+}$ and $8_1^{+}\to 6_1^{+}$ transitions exhibit the opposite trend. We found that this anomalous asymmetry is sensitive to subtle seniority breaking effects, providing a stringent test for state-of-the-art nucleon-nucleon interactions and nuclear models. We analyzed the anomalous asymmetry using VS-IMSRG calculations across various valence spaces. Our ab initio results suggest that core excitations of both proton and neutron across the $Z=50$ shell are ascribed to the observed anomalous seniority breaking in the $N=50$ isotones.