It looks like you might have re-used some components but not “cleaned” them when recycling them. In your Popup, there is a Flex Container (FlexContainer_4) which has an onClick Event which targets the settings Docked View. Remove this onClick Event and your problems will go away.
This Flex Container is almost identical to a Flex Container in the Docked View itself, so it looks to me like you copied the Flex Container from the Docked View and forgot to remove this Event, or update it to close the Popup instead.
To help in diagnosing this in the future, I used the Designer’s Find/Replace tool to search for the id used to manage the Docked View: “settings”. In the following screenshot, you can see the entry which led me to the offending Event.
I confirmed locally that removing the listed event the Docked View behaves as expected.