Debian Policy 4.13 states that Debian packages should not use convenience copies.
Embedded copies (of code, data, fonts or other things) should be removed from the upstream VCS and source tarballs. Upstream might want to only embed the copies in the binary packages they distribute, script the install of their dependencies and or bundle the dependencies into a single but separate source tarball rather than embedding copies of them. Once upstream has fixed the issue, the Debian package can then be updated to the fixed version. If upstream refuse to remove the embedded copies, then Debian should either repack the upstream tarball using Files-Excluded (if there is a DFSG or size issue) or remove the files in debian/rules clean and very early in debian/rules build, so that there is no chance of them being used by the build process.
The list of packages that embed copies (including unused ones) of other projects is maintained in the security-tracker git repository.
This list also contains information about forks so that the security team can check if all forks contain the same vulnerabilities.
All Debian members have commit access to the security-tracker repository and others can send suggestions or additions to the debian-security-tracker mailing list.
check-all-the-things has a couple of tests (embed-readme, embed-dirs) for finding embedded copies via heuristics, and several ideas for new tests.
These wiki pages mention embedded copies: arc4random
These gobby pages mention embedded copies: Teams/Perl/Embedded_modules_in_inc.
The Debian duplication detector detects duplicate files in binary packages and may be useful for detecting verbatim duplication of files across multiple binary packages.
Clonewise is a tool not yet in Debian that could be used to find unfixed vulnerabilities because of embedded code copies. SourcererCC is another tool for detecting embedded code copies. Sokrates can also do duplication detection.
The Debian Sources website collects hashes and ctags of all Debian source code and allows searching for specific hashes and ctags, which may be useful for detecting duplication of source code and data.
If you have a particular file with some interesting aspect (security issue etc) you can likely find other copies using the Debian code search site or external code search engines such as Ohloh code, searchcode and GitHub.
If a file has a fairly unique name, you can often find copies of that file by searching the contents of Debian binary or source packages using apt-file:
apt-file search uniquename.py apt-file search -I dsc uniquename.c
Various Debian folks keep track of embedded copies they found via usertags: