This might be way off since the question is vague, but the only way I could launch an app from bundle is to directly reference the binary inside the .app folder. For example to launch safari, you have to specify the binary /Applications/Safari.app/Contents/MacOS/Safari.

I tried "open /Applications/Safari.app" which works from a terminal window but that results in the exact error described. Using just "/Applications/Safari.app" does nothing.