When running Eclipse tests headlessly, certain dialogs don't show up as they would normally (e.g. when writing/recording the test). This is because of flags:
org.eclipse.jface.dialogsErrorDialog.AUTOMATED_MODE = false;
So if you for example have a test scenario that DOES expect an error dialog to show up, make sure you have above flags set correctly, or find out a different assertion than waiting for an error dialog.