By varying the intrinsic initial geometry, the p/d/$^3$He+Au collisions at the Relativistic Heavy Ion Collider (RHIC) provide a unique opportunity to understand the collective behavior and probe the possible sub-nucleon fluctuations in small systems. In this paper, we employ the hybrid model iEBE-VISHNU with Trento initial conditions to study the collective flow and the fluid behavior in p/d/$^3$He+Au collisions. With fine-tuned parameters, iEBE-VISHNU can describe the $v_2(p_T)$ and $v_3(p_T)$ data from the PHENIX and STAR collaborations. However, for some certain parameter sets with initial sub-nucleon fluctuation, the hydrodynamic simulations have already beyond their limits with the average Knudsen number $\langle K_n \rangle$ obviously larger than one. Our calculations demonstrate that, for a meaningful evaluation of the fluid behavior in the small systems, model simulations should also pay attention to the validity range of hydrodynamics.