I don't think this is unusual at all (in that it's always been thus) and it is why I always check on both Air France and KLM [and 3rd parties] and buy from whichever is the cheapest. The price can also sometimes be lowered by buying from a different country, i.e. Belgium was often cheaper when buying KLM tickets (they didn't have the service fee when it was introduced in NL) but these days I think that difference/loophole has been closed off.
As you say, even the flights that are shown as available can be different.
It certainly pays to shop around.
I guess the explanation is that AF and KL, while related, are still not exactly one and the same, and in some territories/routes they may have different allotments of seats from which they can sell, and you hit a case where KL had a seat left over where AF didn't.