Flow fluctuations in ultrarelativistic heavy-ion collisions can be probed by studying the momentum dependent correlations or the factorization-breaking coefficients between flow harmonics in separate kinematic bins (transverse momentum $p$ or pseudorapidity $\ensuremath{\eta}$). We study such factorization-breaking coefficients for collisions of deformed $^{238}\mathrm{U}+^{238}\mathrm{U}$ nuclei to see the effect of the nuclear deformation on momentum dependent coefficients. We also study momentum dependent mixed-flow correlations for the isobar collision system: $^{96}\mathrm{Ru}+^{96}\mathrm{Ru}$ and $^{96}\mathrm{Zr}+^{96}\mathrm{Zr}$, which have the same mass number but different nuclear structure, thus providing the ideal scenario to study nuclear deformation effect on such observables. We use the TRENTO $+$ MUSIC model for simulations and event-by-event analysis of those observables. We find that these momentum dependent correlation coefficients are not only excellent candidates to probe the fluctuation in heavy-ion collision, but also show significant sensitivity to the nuclear deformation.