The high contrast and spatial resolution requirements for directly imaging exoplanets requires effective coordination of wavefront control, coronagraphy, observation techniques, and post-processing algorithms. However, even with this suite of tools, identifying and retrieving exoplanet signals embedded in resolved scattered light regions can be extremely challenging due to the increased noise from scattered light off the circumstellar disk and the potential misinterpretation of the true nature of the detected signal. This issue pertains not only to imaging terrestrial planets in habitable zones within zodiacal and exozodiacal emission but also to young planets embedded in circumstellar, transitional, and debris disks. This is particularly true for Ha detection of exoplanets in transitional disks. This work delves into recent Ha observations of three transitional disks systems with MagAO-X, an extreme adaptive optics system for the 6.5-meter Magellan Clay telescope. We employed angular differential imaging (ADI) and simultaneous spectral differential imaging (SSDI) in combination with KLIP, a PCA algorithm in post-processing, for optimal starlight suppression and quasi-static noise removal. We discuss the challenges in protoplanet identification with MagAO-X in environments rich with scattered and reflected light from disk structures and explore a potential solution for removing noise contributions from real astronomical objects with current observation and post-processing techniques.