Yes - I wouldn't recommend leaving 'suppress LMS errors' switched on, users will not be notified if something goes wrong and will continue to work through the course thinking that it's all working.
I'd recommend you try to get to the bottom of why the debugger was popping up in the first place.
Are you sure you weren't missing any bits of the log output? You might need to scroll down a bit...
Also, if you press F12 in the course window to open the developer tools and switch to Console you'll get more details than the SCORM debugger shows you. If you're using IE you'll first need to do this.