Machine learning is a field of artificial intelligence (AI) that is becoming essential for several critical systems, making it a good target for threat actors. Threat actors exploit different Tactics, Techniques, and Procedures (TTPs) against the confidentiality, integrity, and availability of Machine Learning (ML) systems. During the ML cycle, they exploit adversarial TTPs to poison data and fool ML-based systems. In recent years, multiple security practices have been proposed for traditional systems but they are not enough to cope with the nature of ML-based systems. In this paper, we conduct an empirical study of threats reported against ML-based systems with the aim to understand and characterize the nature of ML threats and identify common mitigation strategies. The study is based on 89 real-world ML attack scenarios from the MITRE's ATLAS database, the AI Incident Database, and the literature; 854 ML repositories from the GitHub search and the Python Packaging Advisory database, selected based on their reputation. Attacks from the AI Incident Database and the literature are used to identify vulnerabilities and new types of threats that were not documented in ATLAS. Results show that convolutional neural networks were one of the most targeted models among the attack scenarios. ML repositories with the largest vulnerability prominence include TensorFlow, OpenCV, and Notebook. In this paper, we also report the most frequent vulnerabilities in the studied ML repositories, the most targeted ML phases and models, the most used TTPs in ML phases and attack scenarios. This information is particularly important for red/blue teams to better conduct attacks/defenses, for practitioners to prevent threats during ML development, and for researchers to develop efficient defense mechanisms.