I agree, the website is pretty misleading. However, in small print under the big coloured box describing the points earning and other rules it says
Rules may vary for flights operated by a partner airline
.
Regardless, I second
Courmisch's advice. File a formal complaint using the website. Prepare to wait a looooong time before you get any respons. If not happy, file a midleading advertisment complaint to Konsumentverket. They will most probably do nothing, but they might query AY and that might at least prompt them to change the website.
Also, I'm not really sure what points you have got. GOT-TXL is 572km, TXL-ARN is 840. It seems you got ≈72% and ≈54% respectively?!