is there any chances that they wont qualify?
No it's seated on score of Stage 1 + Stage 2
"Top 6 teams from Overall score of Stage 1 and Stage 2, regardless of groups, will advance to Playoffs"
https://liquipedia.net/valorant/VCT/2024/EMEA_League/Stage_2
To give you an exemple, GEN is 3-3, they may be really high on point if they end 4-6 they probably wont go to PO