I've had an issue like this with a partner flight (Swiss sold and operated by LX). Oddly it's stretched out into months that it's not been credited, and the other three segments on the tickets were all credited automatically and without requesting.

I haven't wanted to spend a lot of time on it, but every so often I do either try a missing mileage request or attempt to check on the matter.

I'm flying Swiss again in a few days and wonder whether I will have the same problems this time around. TK Elite (originally through status match but now through earned miles) with possibility to reach Elite Plus if all my flights get credited the way I think the would normally.