Emacs has different behavior depending on whether the highlighting was done with mouse or the keyboard.
Even in transient-mark-mode, if you set the mark and move the point, using backspace will not delete the region.  delete-selection-mode is a minor mode that changes this behavior.
When using the mouse to highlight a region, regardless of delete-selection-mode, using backspace will delete the region that was highlighted with the mouse.  From Section 25.1.1 of the manual:
"While the region remains active, typing  or  deletes the text in that
region and deactivates the mark; this behavior follows a convention established by other 
graphical programs, and it does not apply when you set the region any other way, 
including shift-selection (*note Shift Selection::)."
Based on this, it sounds like you're selecting the region using the mouse.  Is that correct?  Does the same behavior arise when using shift-select-mode or simply using mark and point?