The Lagrangian density for a single real scalar field theory is L=12(∂μϕ)2−V(ϕ)
Specifically (∂μϕ)2=(∂μϕ)(∂μϕ)≠∂μϕ∂μϕ=(∂μϕ)(∂μϕ)+ϕ∂μ∂μϕ
Answer
The notations (∂ϕ)2 and (∂μϕ)2 are shorthands for (∂μϕ)gμν(∂νϕ), where gμν is the inverse metric tensor.
Generally speaking, different authors use different notation concerning how far derivatives act to the right. When in doubt, it is a good idea to insert extra parentheses or spaces in the notation. See also this related Phys.SE post.
However, in the specific context of OP's kinetic term ∂μϕ∂μϕ, it seems universally accepted that it is supposed to mean (∂μϕ)∂μϕ as opposed to ∂μ(ϕ∂μϕ).
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