Closing as "won't fix" due to last upstream comment:
>>>
I'm not sure that anyone should do special handling with those strings. Sure,
ligatures are esthetically pleasing visually. That's why tools like Pango turn
"fi" "fl" "ffl" and etc. into ligatures for display.

However, you shouldn't be using ligatures in your text files. Ligatures are
*glyphs* comprised of multiple characters. That is, you should be using the
"fi" and "fl" characters in your text files and let Pango remap them. Spell
checkers operate at the character/letter level, not the glyph level.
<<<
If you think this is inappropriate, please drop a comment on the bug, where the 
developer read it (https://bugzilla.gnome.org/show_bug.cgi?id=572951). Thanks,

** Changed in: gedit (Ubuntu)
       Status: Triaged => Won't Fix

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ligatures (i.e. fi, fl) not handled very nicely by spell checker
https://bugs.launchpad.net/bugs/333656
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