When you write `:ls` you see all the buffers, not tabs. To remove the buffer you can use `:bd :bdel :bdelete` (see `:help :bdel`) which unloads a buffer and deletes it from the bugger list.
1) in the shell run "vim ."
2) hit "t" on a file
3) type ":bd<enter>"
You still have 2 tabs open. One with the file explorer and one with an empty file. Probably because the file explorer has type "nofile" or something, so vim things the buffer you just closed was the last one. Im not sure why its not closing the tab. It might be a bug.
Is there a way to tell vim "When I type :bd close the frickin tab, even if its the last one!"?