When trying to close an Opportunity, it is best to update it by creating an Estimate or Sales Order from the actual Opportunity record. However, there are instances that users update it manually. It's a common mistake that users edit the Probability field by setting it to 100%. It does update the Document Status to Closed. However, the Status stays at the non-Closed state. Take note that the Status field and Document Status are two different fields as the latter is hard-coded. Having said that, if you need to update an Opportunity, do it using the Status field and not just by changing the values of the Probability field.