If the nanofluid flow rate is equal to water, because the nanofluid density is higher than water, the nanofluid velocity must be lower than water. Your strange results may be due to this.
When the volumetric flow rate of nanofluid and water is the same, then their average velocities are also equal. Viscosity and density of nanofluids are higher than water, and in many nanofluids, the ratio of viscosity to density for nanofluids is higher than water. To summarize, in your study, the Reynolds number of nanofluids is less than that of water, and as you well know, the thickness of the velocity and temperature boundary layers is essentially a function of the Reynolds number, not the mass (or volume) flow rate.