Flip-flop with numbered inputs
They appear to be used to differentiate between three different designs of flip-flop used in the chip. Notice how all the instances of 1 are on the same type of flip-flop, with the same inputs and outputs, but then all the 2s are on a flip-flop that has not only a D input but also S and R inputs. Then all the 3s are on a third type, which have dual S and R inputs each.