This is because a complete binary tree of n nodes does not have height log(n).
Consider a complete binary tree of height k. Such a tree has 2k leaf nodes. How many nodes does it have in total? If you look at each level, you will find that it has 1 + 2 + 4 + 8 + ... + 2k nodes, or 20 + 21 + 22 + 23 + ... 2k.
After some math, you will find that this series equals 2k+1 - 1.
So, if your tree has n nodes, what is its height? If you solve the equation n = 2k+1 - 1 with respect to k, you obtain k = log2(n+1) - 1.
This expression is slightly less nice than log2(n), and it is certainly not the same number. However, by the properties of big-O notation,
log2(n+1) - 1 = O(log(n)).
In the source you are reading, emphasis is given on that the height grows as fast as log(n). They belong to the same complexity class. This information can be useful when designing algorithms, since you know that doubling the input will increase the tree height only by a constant. This property gives tree structures immense power. So even if the expression for the exact height of the tree is more complicated (and if your binary tree is not complete, it will look more complicated still), it is of logarithmic complexity with respect to n.