By default, a dielectric must separate each pair of conductor layers in the cross-section of a design. In rare cases, this does not represent the real, manufactured substrate.
If your design requires you to have conductor layers that are not separated by a dielectric (such as, for half-etch designs), there is a variable that needs to be set in Allegro X APD. You must set this by enabling the variable icp_allow_adjacent_conductors. This entry, and its location in the User Preferences Editor, are shown in the following image.
The Objects on adjacent conductor layers do not electrically connect together, automatically. A via must be used to establish the inter-layer connections.
When enabling this option, it is recommended to exercise caution because excluding dielectric layers from your cross-section can lead to inaccurate calculations, including the calculations for signal integrity and via heights. It is important that your cross-section accurately reflect the finished product to ensure the most accurate results possible. Any dielectric layers present in the manufactured part need to be in the cross-section for accurate extraction, 3D viewing, and so on.
Let us know your comments on the various designs that would require adjacent conductor layers.