The magnetic inhomogeneity of the A-phase in MnSi chiral magnet is identified for the first time from the precise measurements of transverse magnetoresistance (MR) anisotropy. The area inside the A-phase (A-phase core) corresponds to isotropic MR having no confinement to the MnSi crystal lattice. Per contra, the MR becomes anisotropic both on the border of the A-phase and in other magnetic phases, the strongest magnetic scattering being observed when external magnetic field applied along [001] or [00-1] directions. We argue here that the established MR features prove the presence of two different types of the skyrmion lattices inside the A-phase, and the dense skyrmion state of the A-phase core is built from individual skyrmions similar to Abrikosov-type magnetic vortexes.