Additive Manufacturing (AM) of Carbon Fiber-Reinforced Polymer (CFRP) Composites is emerging, with multiple studies focusing on the design and reinforcement mechanisms. Due to the enhanced strength-to-weight ratio of parts and the capability to produce complex geometries, the technology has a huge potential for aerospace and automotive applications. The present article provides insights on the build quality and surface morphology of 3D-printed short carbon fiber-reinforced polymer composites (SCFRPCs) vs continuous carbon fiber-reinforced polymer composites (CCFRPCs). Test specimens are fabricated in an industrial-grade Fused Filament Fabrication (FFF) machine called Markforged X7 with Onyx™ (nylon with short carbon fiber) material and a custom-developed co-extrusion 3D printing system with Markforged continuous carbon fiber and Polylactide (PLA) material. The fiber distribution and arrangement during printing vary depending on the print conditions. The obtained composite’s surface and cross-sectional morphology study effectively explored the failure causes in 3D-printed short and continuous CFRP composites. Fiber clustering and pullouts characterize the short fiber composites, whereas fiber-matrix interface voids contribute to the defects of continuous fiber composites. The reported trends in this study have the potential to provide guidelines for the development of high-quality FFF-fabricated short CFRP composites.