Ligatures are turned as single quotation mark, HELP ME

I'm using ID CS4 in Mac for composing books, so far in two books the ligatures (fi, fl) are turned as single quotation marks in the output export PDF, am unable to find solution for this, looking forward for the solution. Please help me with your great expertise.

Hi Peter,
Thanks for your quick response, let me check and get back to you.
Very first time when it happened we tried again but it was worked well. So this problem is not regular sometimes it works well and sometimes not.
As you have suggested below let me check and get back to you. Thanks.

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