Try cleaning your workspace/projects. Select Project -> Clean from the main menu and then select the "Clean all" radio button and push the "OK" button. This should clear all errors then rebuild all your projects. Hopefully that should remove the duplicate errors.
Just tried this and created an error to test -- still showing 3 lines of the same error.
What is the number and message of the error?
I just mis-spelled my arrayCollection's name.
3 1120: Access of undefined property aptAC.
the correct spelling is apptAC. This produces the error in the problem log 3 times. All errors produce the same 2-3 repeats in the log.