In the Cambridge Advanced Learners Dictionary there is an example:
The Director is currently having talks in the US.
Based on this example can I write:
Currently, I am having two common projects with Mr "A" and Mr "B".
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Have is one of the verbs that can be stative or active depending on their meaning.
If I have a car or a house or a project, then I am trying to say that they belong to me, in which case have expresses possession and is stative.
Here are examples of active meanings: having a shower means taking one, having breakfast means eating, having beer means drinking and having talks means talking or negotiating.
So in your first sentence, have is active and is used in the continuous tense correctly. In the second case, however, you have two projects (stative), and you are working on two projects (active).