The increasing use of fibre reinforced polymer composite materials in a wide range of applications increases the use of similar and dissimilar joints. Traditional joining methods such as welding, mechanical fastening and riveting are challenging in composites due to their material properties, heterogeneous nature, and layup configuration. Adhesive bonding allows flexibility in materials selection and offers improved production efficiency from product design and manufacture to final assembly, enabling cost reduction. However, the performance of adhesively bonded composite structures cannot be fully verified by inspection and testing due to the unforeseen nature of defects and manufacturing uncertainties presented in this joining method. These uncertainties can manifest as kissing bonds, porosity and voids in the adhesive. As a result, the use of adhesively bonded joints is often constrained by conservative certification requirements, limiting the potential of composite materials in weight reduction, cost-saving, and performance. There is a need to identify these uncertainties and understand their effect when designing these adhesively bonded joints. This article aims to report and categorise these uncertainties, offering the reader a reliable and inclusive source to conduct further research, such as the development of probabilistic reliability-based design optimisation, sensitivity analysis, defect detection methods and process development.