Eigen makes extensive use of expression templates in C++ to collapse complex operation sequences into streamlined and minimal calculations. This is generally ok, until you need a debug build. I've regularly seen debug builds of software using Eigen run 1000x to 10000x slower than the release build, which seriously complicates various debugging workflows. It also makes it a nightmare to run your test suite through valgrind, for example.
I've seen several engineers attempt (and fail) to try creating/linking a release build of Eigen with a debug build of the rest of the program to try to regain most of that speed while still allowing a decent amount of debugability, but this is really hard due to all the aggressive inlining and heavy use of templates.
In my experience, I would happily accept a 2x or more slowdown in linear algebra performance in release builds in exchange for significant boost in debug execution speed. If you're starting a greenfield project, you should consider how important decent debug performance is before choosing Eigen by default.