Homebrew development is as subject to bugs as old software was, but many suffer from additional compatibility problems with the NES hardware due to being tested on emulators exclusively. It is often the case that early homebrew ROMs will not run correctly on hardware. Since the release of the PowerPak in 2008, and general improvement in emulators over time, these problems have become less frequent.
For a partial list of homebrew projects, see: Projects
This is a list of issues that commonly appear due to lack of popular support in emulators, or sometimes even hardware limitations of flash-carts like the PowerPak. Many emulators are merely trying to be compatible with existing games, rather than accurately reflecting the hardware, making them inadequate for verifying the correctness of new software.