Some applications do not appear as a source for system audio sharing until they have actually made an audible sound on your Mac. For example, if you're trying to share a video in Google Chrome, but Chrome hasn't yet made a sound through your speakers (or your chosen sound output) you might receive the following error:
In this case, Ecamm will fall back on capturing all audio that plays through your system output, including the desired application.
To select just the application you want to share, play a sound in that application and try again. You can avoid the problem entirely by ensuring you have launched the desired application and played out a sound before your recording or stream.