The issue concerning the nature and the role of microstructural inhomogeneities in iron chalcogenide superconducting crystals of FeTe_0.65Se_0.35 and their correlation with transport properties of this system was addressed. The presented data demonstrate that chemical disorder originating from the kinetics of the crystal growth process significantly influences the superconducting properties of an Fe-Te-Se system. Transport measurements of the transition temperature and critical current density performed for microscopic bridges allow us to deduce the local properties of a superconductor with microstructural inhomogeneities, and significant differences were noted. The variances observed in the local properties were explained as a consequence of weak superconducting links existing in the studied crystals. The results confirm that the inhomogeneous spatial distribution of ions and small hexagonal symmetry nanoscale regions with nanoscale phase separation also seem to enhance the superconductivity in this system with respect to the values of the critical current density. Magnetic measurements performed in order to determine, in an alternative way, the values of the critical current density, as well as to find the relaxation rate and to check the scaling of the pinning force, confirm the conclusions drawn from the transport measurements.