First of all as you remark above, it is easy to see by elementary means that the error is at most $2^k$. It was an old conjecture of Erdos that this error term could be improved to $o(2^k)$. However this conjecture turns out not to be true!
In 1951 Vijayaraghavan proved that the error term $O(2^k)$ is best possible in the sense that for any $k\in\mathbb{N}$ and $\delta >0$ you can find an integer $n$ with exactly $k$ distinct prime factors, and a real number $x$, such that
$$\Phi(n,x)>2^{k-1}-\delta.$$$\Phi(n,x)-xr>2^{k-1}-\delta.$$
Vijayaraghavan's paper is On a problem in elementary number theory. J. Indian Math. Soc. 15, (1951).
For a more detailed and up to date discussion you could look at the more recent paper Codecà, Nair, An extension of a result of Lehmer on numbers coprime to n. Ramanujan J. 16 (2008), no. 1, 59–71.

