Aegean Airlines Miles&Bonus - Earning on LX

Just done MAN-ZRH-BEG-ZRH-MAN in D on LX.

Only been credited the outbound sector so far, but only tier miles of 2432.

According to the Lufthansa miles and more site it should be 8000 so why only 4864 on Aegean?

Because the Lufthansa site informs Miles & More members what they will earn in the Miles & More programme.

You did not credit to that programme. You have earned according to A3's Miles&Bonus earning chart.

On LX metal, D class, M&M gives you 200% of the distance flown with a minimum of 2000 miles.
M&B gives you 200% of the distance but the minimum is only 1000.
These rules are clearly stated on both LH and A3 websites.
If you're not happy with that, your only option is to have your return flight credited on M&M...

My mistake: M&M gives you a flat 2000 miles per flight, whatever the mileage.

LX will give you 2000 miles per segment, thus 8000 total (plus 25% if you have status). But on a 4 segment intraeuropean trip with a *A partner, they will not give you that, but less, similar to what A3 does. This is info is known through the programmes' description beforehand, and one decides accordingly which airline to fly and where to credit the miles.