Fair play to the affiliate. I've seen this happen to benefit us (very rarely) & it wasn't deliberate .... & other colleagues too.
Whether it was or wasn't good luck to them.
Some merchants make the mistake of thinking they have rights on natural search in search engines & more foolishly think they get 100% click thru rates from natural search.
If this merchant is complaining, in my book, it sounds like they begrudge paying commissions if they are giving you a hard time over it.
If there is a way, I would like to know too.