when there is no copper between the components they are not connected, so, when you unfill the zones, you take the copper away and they are not connected, when you fill up the zones again, the copper is again there and then they are connected.
If your zones would be filled up and still you notice some suspicious rastnet, then you will need to look what is going on.
p.s. the ERC will fill up the zones automatically before telling you if a connection between component is missing or not.
EDIT: I liked the way eelik put it better