What is com.apple.launchctl.Aqua?
com.apple.launchctl.aqua is launchctl. If you run strings over launchctl in /bin/launchctl it returns Aqua in amongst other strings. 

I would say another script is trying to load and launchctl is failing to do so which is why you've got that error message. 

I would list what processes are loaded and see if anything that is in your agent/daemon dirs isn't loading as expected.