If you have AppleCare+ Protection Plan and used the Express Replacement service it's typically $99 unless you don't send your old iPhone back within the 10 days in which case they charge you the full value of the iPhone.
But, it is $99 if you use the express replacement, even if the issue would have been covered by the normal warranty for non-accidental damage. But to get normal (non-accidental) warranty service for free (for non-accidental damage) you have to do the regular mail-in warranty service option where they only send you an empty return box at first, not the "express" option.
It sounds like the Apple support person didn't explain it sufficiently to you. The $99 is for paying for the convenience (either for covered warranty damage, or non-covered accidental damage) to get a replacement iPhone sent to you in advance. The "normal" free warranty service option is they send you an empty box, you send in the iPhone and return it, and once they receive it you get your replacement. With that you are out an iPhone for a week or so. The $99 saves you a week or so of downtime without a phone.
Is this what happened and the Apple support person just didn't explain that this would cost you no matter what?