Policy scoping reviews are an effective method for generating evidence-informed policies. However, when applying guiding methodological frameworks to complex policy evidence, numerous, unexpected challenges can emerge. This paper details five challenges experienced and addressed by a policy trainee-led, multi-disciplinary research team, while conducting a scoping review of youth Human Immunodeficiency Virus and Hepatitis C primary and secondary prevention policies, which occurred across and within sectors and jurisdictions in Atlantic Canada. How these challenges were addressed is described, as are suggestions for how the lessons learned may provide guidance to other policy scoping reviews. Implications for future directions are also discussed.