I'm doing some classical field theory exercises with the Lagrangian $$\mathscr{L} = -\frac{1}{4}F_{\mu \nu}F^{\mu \nu}$$ where $F_{\mu \nu} = \partial_\mu A_\nu - \partial_\nu A_\mu$. To find the conjugate momenta $\pi^\mu_{\ \ \ \nu} = \partial \mathscr{L} / \partial(\partial_\mu A^\nu)$, I can use two methods.
First method: directly apply this to $\mathscr{L}$. We get a a factor of $2$ since there are two $F$'s, and another factor of $2$ since each $F$ contains two $\partial_\mu A_\nu$ terms, giving $$\pi^\mu_{\ \ \ \nu} = -F^\mu_{\ \ \ \nu}$$$$\pi^\mu_{\ \ \ \nu} = -F^\mu_{\ \ \ \nu}.$$
Second method: get $\mathscr{L}$ in terms of $A$ by expanding and integrating by parts, yielding $$\mathscr{L} = \frac{1}{2}(\partial_\mu A^\mu)^2 - \frac{1}{2}(\partial_\mu A^\nu)^2$$$$\mathscr{L} = \frac{1}{2}(\partial_\mu A^\mu)^2 - \frac{1}{2}(\partial_\mu A^\nu)^2.$$ Differentiating this gets factors of $2$ and gives $$\pi^\mu_{\ \ \ \nu} = \partial_\rho A^\rho \delta^\mu_\nu - \partial^\mu A_\nu$$$$\pi^\mu_{\ \ \ \nu} = \partial_\rho A^\rho \delta^\mu_\nu - \partial^\mu A_\nu.$$
These two answers are different! (They do give the same equations of motion, at least.) I guess that means doing the integration by parts changed the canonical momenta.
Is this something I should be worried about? In particular, I have another exercise that wants me to show that one of the canonical momenta vanishes -- this isn't true for the ones I get from the second method! Plus, my stress-energy tensor is changed too. When a problem asks for "the" canonical momenta, am I forbidden from integrating by parts?
