On two of the projects I'm working with lately, we have almost every single library pulled into the source tree. Why? In some cases, we have bugs to fix that will take months just to get upstreamed in the respective project, and possibly years before you find them in all non-legacy releases of the popular Linux distributions.
In other cases, we have have changes or customizations that upstream doesn't even want, requiring that we not only fork the project but then get enough mindshare from the community to have the same support network as well as getting distributions to even package the library.
Yet other cases are libraries that are designed to be bundled because they do not attempt to provide a stable API or sufficient run-time configuration of options (this one happens a lot more often than I'd like).
And yet other cases are small technical integration needs (inlining w/ LTO a matrix math library, for instance, can have such a huge impact on performance that using it as a shared library is downright stupid).
I don't for a second believe any of those are common issues, but they do happen.