When you edit a manual grade item on the gradebook setup page it gives you a pop up window to make quick changes. If you need to make more changes there is a show more button which takes you to the full settings page for the grade item. If you make any update in the pop up window or even just hit save without making any updates it changes that grade item to extra credit. If you open the pop up window again and disable extra credit and save it does not go away. You have to open the pop up window and click on show more and then uncheck the extra credit box from the full settings page for the grade item. 
 
I could not find a specific bug tracker for this but it could be related to these 2.
https://tracker.moodle.org/browse/MDL-48187?focusedCommentId=351476&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel
https://tracker.moodle.org/browse/MDL-66838
 
 
Scope of Issue
Sites on 4.3
 
Steps to Replicate/Observe

The main category has to be set to weighted mean of grades and the sub category the grade item is in has to be set to simple weighted mean of grades. Then the grade item gets updated to extra credit if you save anything in the modal window even with extra credit not checked.

• Go to any course
• In the course, go to the Gradebook setup page
• Edit a Manual Grade Item:

• • Identify a manual grade item in the Gradebook setup.
  • Click the Edit dropdown next to the grade item and select Edit settings.
  • A pop-up window will appear, allowing you to make quick changes.
• Attempt to Save Changes:

• • In the pop-up window, either make a change or simply click the Save changes button without making any modifications.
• Check the Extra Credit Status:

• • Notice that the grade item is now marked as Extra Credit even if no changes were made related to extra credit.
• Attempt to Disable Extra Credit:

• • Reopen the pop-up window for the same grade item by clicking Edit settings again.
  • Uncheck the Extra Credit box in the pop-up window and click Save changes.
• Verify the Issue:

• • Observe that the grade item remains marked as Extra Credit despite unchecking the option in the pop-up window.
• Resolve the Issue:

• • Open the pop-up window for the grade item one more time.
  • Click on the Show more... button to access the full settings page for the grade item.
  • Uncheck the Extra Credit box in the full settings page.
  • Click Save changes to finally disable the extra credit status.