I am trying to connect two points of my board with a bottom and top route, connected with a via. Whenever I link the two routes, a yellow x appears. Placing the via on top of the connection doesn't fix it.
How can I get rid of it?
The via doesn't get the same ID as the route. You should try to inspect the name of the route and via and make them the same. You could also try to draw a new route using nets and just change the layer on the point you want to go from top to bottom (or from bottom to top) and eagle will automatically add a via