Ligatures are broken
OpenType ligatures are broken in Illustrator. When the ligatures feature is enabled most ligatures remain different letters. If ligatures are input directly from the glyphs palette they will decompose into different letters. Even if ligatures are disabled they still decompose into different letters when input from the glyphs palette.
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James Puckett
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James Puckett commented
Nevermind this post. It turns out Illustrator disables ligatures when positive tracking is applied to text.