We propose a novel solution combining supervised and unsupervised machine learning models for intrusion detection at kernel level in cloud containers. In particular, the proposed solution is built over an ensemble of random and isolation forests trained on sequences of system calls that are collected at the hosting machine's kernel level. The sequence of system calls are translated into a weighted and directed graph to obtain a compact description of the container behavior, which is given as input to the ensemble model. We executed a set of experiments in a controlled environment in order to test our solution against the two most common threats that have been identified in cloud containers, and our results show that we can achieve high detection rates and low false positives in the tested attacks.