A wealth of literature exists on control allocation algorithms for over-actuated air vehicles, launch vehicles, and spacecraft's. Most of these algorithms focus primarily on minimizing some objective function such as command tracking error and/or control effector usage. Linear allocators (pseudo inverses) are usually the conventional choice due to their simplicity and the ability to achieve a significant portion of the theoretical moment/impulse space. Generally, it is assumed that there exists minimal interaction effects between control effectors. In fact, very few studies address the problem of control effector interactions in the context of control allocation, especially for small spacecraft's with a reaction control system (RCS). This paper presents a CubeSat RCS design with a four thruster tetrahedral layout such that when two or more thrusters re, the resultant impulse differs noticeably compared to the sum of the contributions from individual thruster rings. This undesirable effect is caused by the design of the propellant tank and regulator. To mitigate this issue, an innovative modified pseudo inverse (MPI) control allocation algorithm was developed that adjusts the pseudo inverse solution based on test data. The algorithm is iteration-free and superior to the standard pseudo inverse in minimizing the command tracking error.