Recent observations of helioseismic holography revealed that magnetic fields that are inclined relative to the line-of-sight direction could cause systematic variations in measured acoustic phase shifts ( hereafter, inclined magnetic field effect) and that the presence of surface magnetic field may shift the phases and impair the coherence of acoustic waves ( known as the showerglass effect), thus complicating the interpretation of acoustic wave propagation time through the solar interior. In this paper we examine how these two observational effects affect time-distance helioseismology measurements in magnetic regions. It is confirmed that the inclined magnetic field could cause variations in time-distance measured acoustic travel times inside sunspot penumbra as well; however, inversions of the measured times for the wave propagation show that this effect only slightly shifts the location of negative sound-speed variations near the solar surface but basically does not change the inverted deeper interior structures. Further measurements using continuum intensitygrams and line-depth data from the MDI on board SOHO illustrate that the inclined magnetic field does not cause any obvious systematic travel-time variations in these observations. Regarding to the showerglass effect, we find that outgoing and ingoing travel-time perturbations through sunspots from our typical time-distance measurements are significantly smaller than those reported from helioseismic holography and also strongly depend on the propagation depth indicating deep changes. In addition, our second-skip cross-correlation experiments demonstrate that inside sunspots, the half of the double-skip travel times are very similar to the mean single-skip travel times, indicating that acoustic signals observed inside sunspots do not introduce detectable phase shifts after applying proper phase-speed filtering.