The analyzer found a source file or an object with a name containing characters like '[', ']', '(', or ')'. These characters are removed leading to duplicate names. This message can be also generated when the analysis option "Platform: IBM z/OS" is set to true and the source code comes from another platform that allows using long names. In that case, names are truncated to 8 characters leading to duplicated names.
Having duplicate names prevents to resolve references.

Select the object <INCLUDE_NAME> in the list of objects in the Unknown\Copybooks folder of the technical browser in CAST Enlighten to see where it is referenced. If this is an application specific copybook, then it is recommended to ask the application team for it. This could affect reference resolution and any quality rules you might want around data components.

You will find the complete list of missing source elements at the end of the analysis log.

Open the source file. Check if it contains COBOL code.
If yes, then verify if the Starting Column analysis parameter is set properly. It is possible to have copybooks that do not have the same Starting column than calling programs. In this case, adapt the copybook to the expected format.
If no, then remove file from the analyzed folder and exclude it from source selection. Generally, this means that source code from other technology than Cobol has been delivered in the folder. If you select source code via directories, then the analyzer is going to take into account all files belonging to this directory.

Select the object <OBJECT_NAME> in the list of objects in the Unknown\<OBJECT_TYPE> folder of the technical browser in CAST Enlighten to see where it is referenced. If this is an application specific element, then it is recommended to ask the application team for it. It can affect any quality rules.

If the object is a program, it can be called through its PROGRAM-ID name (this is the most frequent case) which is different from its source file name. In this case you must search for it by using a GREP tool.

If the message is about a reference to a DD name, then check if there is a JCL step calling the program and defining a DD card with the same DD name. If there is no such JCL element and if there is a supported batch part, then ask the application team for it. Note that the resolution of this type of links is not supported in case the program for which the message has been emitted is a subprogram and you can ignore that message. If the program is a main batch program and there is a JCL step that calls it, then please contact the CAST Support.

You will find the complete list of missing source elements at the end of the analysis log.

Check if the JCL code containing the referred DD card has been delivered and is part of the analysis scope. It could be the case for JCL external procedures. 

Remove corresponding source files from the source files folder.
Note that the list of supported COBOL version is available in the documentation.