Well you know to get a 100 chemistry all players must have 9 chemistry rite, well players can actualy achieve chemistry of 11, not 9, so it does not matter if everyone doesnt link up properly, because the players who achieve 11 chemistry will make the chemistry up.
Use the right analog to go across to 'Chemistry' on your squad, then press 'X' that is the actual chemistry, some players will achieve 11 chemistry if they match up perfectly, Nation,League and Club all the same, but this doesnt show up on the cards unless you press 'X' (Actions button) and you will see some of your players may have 11 chemistry which is the best they can be.