Branches do not cause any ambiguity but illustrate that distance in the SMILES string does not equate to distance from an atom back to the root atom. For example, c1c(F)cccc1 and c1c(cccc1)F are written as cc(F)cccc6 and cc(cccc6)F respectively, but the distance in the SMILES string between the ring-opening and ring-closing atoms is 7 and 6 respectively. One way to think of this is that when counting back to find the ring-opening atom, you should ignore atoms in other branches.