Patenting by itself is no harm. Many open-source licenses grant an explicit or implicit patent license to the source code. So, open-source + patented is certain

Patenting by itself is no harm. Many open-source licenses grant an explicit or implicit patent license to the source code. So, open-source + patented is certainly possible. A recent example is the case where Google bought patent license from MPEG-LA for VP8 codec. And then Google sublicensed it, giving a royalty-free patent license for every user of VP8 codec, along with the source code.