Despite its technological benefits, Internet of Things (IoT) has cyber weaknesses due to the vulnerabilities in the wireless medium. Machine learning (ML)-based methods are widely used against cyber threats in IoT networks with promising performance. Advanced persistent threat (APT) is prominent for cybercriminals to compromise networks, and it is crucial to long-term and harmful characteristics. However, it is difficult to apply ML-based approaches to identify APT attacks to obtain a promising detection performance due to an extremely small percentage among normal traffic. There are limited surveys to fully investigate APT attacks in IoT networks due to the lack of public datasets with all types of APT attacks. It is worth to bridge the state-of-the-art in network attack detection with APT attack detection in a comprehensive review article. This survey article reviews the security challenges in IoT networks and presents the well-known attacks, APT attacks, and threat models in IoT systems. Meanwhile, signature-based, anomaly-based, and hybrid IDSs are summarized for IoT networks. The article highlights statistical insights regarding frequently applied ML-based methods against network intrusion. Finally, open issues and challenges for common network intrusion and APT attacks are presented for future research.