The azimuthal angular dependence of the in-plane magnetoresistance provides a powerful probe for detecting rotational symmetry breaking in superconductors, which has significant implications for understanding the superconducting pairing symmetry and the intertwined orders. However, in two-dimensional or layered superconductors with strong anisotropy between in-plane and out-of-plane critical fields, measuring the in-plane magnetoresistance is particularly challenging as it is extremely sensitive to the field misalignment. Here we perform systematic electrical transport measurements on ultrathin FeSe films grown on SrTiO3 substrates. By remounting the same FeSe film to change the field misalignment, two qualitatively different angular dependences of the in-plane magnetoresistance are observed in the superconducting transition region, indicating the extreme sensitivity of the measurement to field misalignment. The observed anisotropic in-plane magnetoresistance can be well captured by our geometric model considering the field misalignment effect. Our work provides a practical framework for disentangling misalignment effect and investigating the in-plane rotational symmetry breaking in two-dimensional or layered superconductors.