It sounds like you are running up against a bug, because when you delete a track in the track view, the corresponding mixer channel in the mixer view should disappear also.
If you don’t have any content in this document, I suggest you just create a new document. (One of the big advantages of Logic is the templates, so choose the right template for what you are doing carefully and you may not even have to manage any tracks.)
If you do have content in the document, one thing you can try is to Save the document, then Close it, and in Finder, first duplicate your document to make a backup, and then context-click (2-finger tap or right-click) the original document and choose “Show Package Contents” from the pop-up menu and the document will open as a folder. Inside, there are files and folders. Go into the “Alternatives” folder, then into the “000” folder, and find a file called “DisplayState.plist” and put that file in the Trash. Then close the windows you just created.
The “DisplayState.plist” file contains a bunch of options for how your document should be displayed by Logic, and it is the source — unfortunately — of some Logic Pro X bugs. By putting it in the Trash, you reset the non-content parts of your document to being a new document.
Then open your document in Logic and with any luck the phantom channels will be gone from the mixer.