I think the issue is that the defending team was also encroaching, which should have called for a retake. Which was the point. VAR looked at the encroachment of the attacker, and ignored the encroachment by the defenders.
A story in English, which gives some more detail...
Apparently:
https://www.krcgenk.be/nl/nieuws/5438/anderlecht-krc-genk-wordt-herspeeld
Translation (according to my browser, YMMV):
From what I can gather, during the game a penalty was taken by Genk, it was saved, but another Genk player scored on the rebound. But the ref disallowed it...