Teams will only advance to the next round if the 'Advance Positions' have been set.
Go to the 'Matches' tab for your Group Stage Cup
Press on the tab: 'Group Stage Matches'
Once all the matches have been played and you know how the winning team or teams are, you can select their 'Advance Position'
Press update
Repeat this for all groups
Next, check your round advancement settings
In the 'Rounds' page make sure that you have the correct advancement settings, by default only position 1 teams go through to the Knockout Stage, you might want teams that finish second place in a group also advance into the Knockout Stage.
To change this click on the link: 'change how teams enter this round' for the first round of your Knockout Stage
In the dropdown select 'Stage: Group Stage, Round: Group Stage, Position: 2'
Then press 'Add'
Now 2 teams from each group will progress into the Knockout Stage.