As long as all the wires are on the same phase then yes, you can pass multiple wires through the same Current Transformer (CT). It is critical that all the wires are on the same phase, so you should double check this before setting up your meter in this way.
You can have multiple wires from the same phase going through each CT (see the attached). In this example there are 2 hot phases L1 and L2. Multiple black wires from L1 go through CT1 and multiple red wires from L2 go through CT2. The amperage in the wires from the same phase will combine together and will be accurate. All wires passing through a CT should not exceed the amperage rating of the CT. If you combine wires from different phases in the same CT they will cancel each other out.
You can also use multiple CTs on the same phase. Here is an explanation of how to use multiple CTs per phase