While in the Org Agenda, and navigating to the end of line for a given item
(assuming more than one todo items), and calling org-agenda-todo (with
keybindings t, or C-c C-t)... this result in the call being applied to the
next line item, instead of the one the cursor is on.

This only happens when the cursor is at the end of the line.

I would consider this to be a bug.

Regards,
Daniel