We use SQL dacpacs for database references in our SQL Data Tools projects. Sometimes the database we need to reference is a vendor database with loads of issues in it, so if we try and extract a dacpac using management studio, it just bombs out with an ugly exception. I have seen all kinds of issues when doing this.
Your first though may be to re-create the database using scripts and only include the objects that you need. That works but it's a bit of a pain to look after. What we really need is way to extract the dacpac, warts and all, and the only way I know how to do that is by using the SqlPackage.exe command line tool.
Use the following to extract a simple dacpac for a reference:
C:\Program Files (x86)\Microsoft SQL Server\130\DAC\bin\SqlPackage.exe /Action:Extract /SourceServerName:SQLCLUSTER3 /SourceDatabaseName:$(DbName) /TargetFile:"C:\Temp\$(DbName) .dacpac"