Anomalies displaying significant deviations between terrain elevation products acquired from spaceborne full-waveform LiDAR and reference elevations are frequently observed in assessment studies. While the predominant focus is on “normal” data, recognizing anomalies within datasets obtained from the Geoscience Laser Altimeter System (GLAS) and the Global Ecosystem Dynamics Investigation (GEDI) is essential for a comprehensive understanding of widely used spaceborne full-waveform data, which not only facilitates optimal data utilization but also enhances the exploration of potential applications. Nevertheless, our comprehension of anomalies remains limited as they have received scant specific attention. Diverging from prevalent practices of directly eliminating outliers, we conducted a targeted exploration of anomalies in forested areas using both transmitted and return waveforms from the GLAS and the GEDI in conjunction with airborne LiDAR point cloud data. We unveiled that elevation anomalies stem not from the transmitted pulses or product algorithms, but rather from scattering sources. We further observed similarities between the GLAS and the GEDI despite their considerable disparities in sensor parameters, with the waveforms characterized by a low signal-to-noise ratio and a near exponential decay in return energy; specifically, return signals of anomalies originated from clouds rather than the land surface. This discovery underscores the potential of deriving cloud-top height from spaceborne full-waveform LiDAR missions, particularly the GEDI, suggesting promising prospects for applying GEDI data in atmospheric science—an area that has received scant attention thus far. To mitigate the impact of abnormal return waveforms on diverse land surface studies, we strongly recommend incorporating spaceborne LiDAR-offered terrain elevation in data filtering by establishing an elevation-difference threshold against a reference elevation. This is especially vital for studies concerning forest parameters due to potential cloud interference, yet a consensus has not been reached within the community.