Unmanned Aerial Vehicles (UAVs) are becoming more dependent on mission success than ever. Due to their increase in demand, addressing security vulnerabilities to both UAVs and the Flying Ad-hoc Networks (FANET) they form is more important than ever. As the network traffic is communicated through open airwaves, this network of UAVs relies on monitoring applications known as Intrusion Detection Systems (IDS) to detect and mitigate attacks. This paper will survey current IDS systems that include machine learning techniques when combating various vulnerabilities and attacks from bad actors. This paper will be concluded with research challenges and future research directions in finding an effective IDS system that can handle cyber-attacks while meeting performance requirements.