I've been confused about the $\partial_{\mu}$ operator.
Peskin and Schroeder defines it as $\partial_{\mu} = \frac{\partial}{\partial x^{\mu}}$
For example, the Euler Lagrange equation of motion is
$$ \frac{\partial}{\partial x^{\mu}}\Big( \frac{\partial \mathcal{L}}{\partial (\partial \phi/\partial x^{\mu})}\Big) - \frac{\partial\mathcal{L}}{\partial \phi} = 0$$
If we apply this to the Lagrangian
$$ \mathcal{L} = \frac{1}{2}(\partial_{\mu} \phi)^2 - \frac{1}{2}m^2 \phi^2$$
Then
$$ \frac{\partial \mathcal{L}}{\partial (\partial \phi/\partial x^{\mu})} = \frac{\partial \mathcal{L}}{\partial(\partial_{\mu} \phi)} = \partial_{\mu}\phi$$
And thus the first term should be $$ \partial_{\mu} \partial_{\mu} \phi$$
But the first term in the Klein Gordon equation is
$$ \partial^{\mu} \partial_{\mu} \phi$$
Where am I going wrong here? How do contravariant and covariant tensors and the Minkowski metric tensor apply?
[Edit]
Follow up question:
$$\partial_{\mu}\Bigg(\frac{\partial \mathcal{L}}{\partial (\partial_{\mu} \phi)}\Bigg) = \partial_{t}\Bigg(\frac{\partial \mathcal{L}}{\partial (\partial_{t} \phi)}\Bigg) + \partial_{x}\Bigg(\frac{\partial \mathcal{L}}{\partial (\partial_{x} \phi)}\Bigg)$$
But if
$$ \frac{\partial \mathcal{L}}{\partial (\partial_{t} \phi)} = \partial_{t} \phi = \partial^{t} \phi$$
And
$$ \frac{\partial \mathcal{L}}{\partial (\partial_{x} \phi)} = -\partial_{x} \phi = \partial^{x} \phi$$
Then
$$\partial_{\mu}\Bigg(\frac{\partial \mathcal{L}}{\partial (\partial_{\mu} \phi)}\Bigg) = \partial_{t} \partial^{t} \phi + \partial_{x} \partial^{x} \phi$$
We seem to missing a minus sign here. Where's the mistake?