I think your problem happens because of duplicated Node or Element IDs. Each Mesh begins automatically with Node ID 1 and Element ID 1. If you then join different meshes inside an assembly Mesh, you have duplicated element or node IDs. To resolve this, inside you assembly FEM, rightclick on your AFEM inside the Simulation Navigator and start the Assembly Label Manager (else refer to Search Function). Inside this Tool, you can reset the Node and Element IDs. When everything is ok, Green Check-Symbols should appear. You can also make use of the the Run Verification and Automatically Resolve tools.
Hope this works