Here is perhaps the simplest example.  Let $A$ be the C*-algebra of all sequences of $2 \times 2$ matrices converging to a scalar multiple of diag(1,0).  Let $p$ be the constant sequence diag(1,0), and q a sequence of rank 1 projections converging to diag(1,0) but never exactly equal.  Then $p$ and $q$ have no supremum at all.  This example can be tweaked to make it unital by allowing any limit matrix at infinity and taking $q$ to alternate diag(1,0) and nearby but unequal projections.  Then $p$ and $q$ have no least upper bound.