Additive manufacturing (AM) defects present significant challenges in fiber-reinforced thermoplastic composites (FRTPCs), directly impacting both their structural and non-structural performance. In structures produced through material extrusion-based AM, specifically fused filament fabrication (FFF), the layer-by-layer deposition can introduce defects such as porosity (up to 10–15% in some cases), delamination, voids, fiber misalignment, and incomplete fusion between layers. These defects compromise mechanical properties, leading to reduction of up to 30% in tensile strength and, in some cases, up to 20% in fatigue life, severely diminishing the composite’s overall performance and structural integrity. Conventional non-destructive testing (NDT) techniques often struggle to detect such multi-scale defects efficiently, especially when resolution, penetration depth, or material heterogeneity pose challenges. This review critically examines manufacturing defects in FRTPCs, classifying FFF-induced defects based on morphology, location, and size. Advanced NDT techniques, such as micro-computed tomography (micro-CT), which is capable of detecting voids smaller than 10 µm, and structural health monitoring (SHM) systems integrated with self-sensing fibers, are discussed. The role of machine-learning (ML) algorithms in enhancing the sensitivity and reliability of NDT methods is also highlighted, showing that ML integration can improve defect detection by up to 25–30% compared to traditional NDT techniques. Finally, the potential of self-reporting FRTPCs, equipped with continuous fibers for real-time defect detection and in situ SHM, is investigated. By integrating ML-enhanced NDT with self-reporting FRTPCs, the accuracy and efficiency of defect detection can be significantly improved, fostering broader adoption of AM in aerospace applications by enabling the production of more reliable, defect-minimized FRTPC components.