Cold, velocity-controlled molecular beams consisting of a single quantum state promise to be a powerful tool for exploring molecular scattering interactions. In recent years, Stark deceleration has emerged as one of the main methods for producing velocity-controlled molecular beams. However, Stark deceleration is shown not to be effective at producing a molecular beam consisting of a single quantum state in many circumstances. Therefore, quantum state purity must be carefully considered when using Stark decelerated beams, particularly in collision experiments where contributions from all quantum states must be addressed.