Issue with the Connect Line Tool

[micheus]

Your object is "corrupted". The down side you were try to connect have some strange connections with many faces overlapped. Check it after I extract it and move the faces:


Here is what you can do for fix it:

You have to select the edge loop as pointed in the 2st image and then try F6 or F7 in order to get the selection as in the 3rd image; Then apply the context menu Loop Cut; The result you see in the 4th image. After you remove the corrupted object now separated, select the top face as in 5th image and Extrude it once to get back that removed area.