In this Dark Souls 2 Wiki it says that sometimes it costs 0 souls to be granted a pardon.
On that same wiki but on the page about sins, it states that this is a glitch that seem to have started when the Crown of the Ivory King DLC was released:
Cromwell the Pardoner does not reset your sin level. His pardon mechanic only removes the aggro from hostile NPCs. However, due to a glitch that erroneously caused sin in the Crown of the Ivory King DLC during Patch 1.08, Cromwell was changed to offer 1 pardon for free. Unlike the regular pardon described above, it completely clears all types of Sinner statuses. It can only be done once per character.
I'm guessing this is what happened. To verify, all your sinner statuses should be reset if this is the case.
I also found a Steam Post of a player talking about the same thing and some people have mentioned that it is a glitch that seem to have occured with the DLC being released. Since you have the Scholar of the First Sin edition (at least you have it tagged), you have the DLCs, and I'm betting that glitch occurred.