One big drawback is the extra complexity -- 3D engines don't always have the same level of first-class support for 2D graphics as dedicated 2D engines would. This means that it's either a lot of extra work to deal with composing and managing a 2D scene, and/or you're still having to deal with the complexity of the 3D math and transformation pipeline. Especially if you're not entirely familiar with the fundamentals of 3D graphics theory, you can find yourself lost and confused when your images don't show up and if you are not careful, you can stumble on to a "solution" that makes your images appear but isn't necessarily correct (and will thus bite you later on).
But beyond the human aspect, as long as the 3D engine has the tools you need to build your 2D game, it's not a bad idea to use one. They are far more prevalent these days and tend to be developed more aggressively, so that's a plus. Additionally there are probably still a handful of 2D-focused engines or frameworks out there that aren't using D3D or OpenGL behind the scenes, and thus may not be getting the benefits of modern GPUs.
In this related question you can see a lot of discussion about what might make 3D more difficult (you will only have to deal with a subset of that were you to only use the 3D engine for a 2D game though).