I think you are starting with the expression $$T^{\mu\nu}=\frac{\partial\mathcal{L}}{\partial(\partial_\mu\phi)}\partial^\nu\phi-\eta^{\mu\nu}\mathcal{L}$$Then you are saying that at present you are only interested in the three spacelike on-diagonal components in an Einstein coordinate system, which are$$T^{ii}=\frac{\partial\mathcal{L}}{\partial(\partial_i\phi)}\partial^i\phi-\eta^{ii}\mathcal{L}$$where ##i=1,2,3## and no summation convention is assumed. Note that this is not a tensor expression. It is simply three expressions stating a relationship between ##\mathcal{L}##, ##\phi## and specific components of ##T##. That is, this is explicitly these three expressions:$$\begin{eqnarray*}
T^{11}&=&\frac{\partial\mathcal{L}}{\partial(\partial_1\phi)}\partial^1\phi-\eta^{11}\mathcal{L}\\
T^{22}&=&\frac{\partial\mathcal{L}}{\partial(\partial_2\phi)}\partial^2\phi-\eta^{22}\mathcal{L}\\
T^{33}&=&\frac{\partial\mathcal{L}}{\partial(\partial_3\phi)}\partial^3\phi-\eta^{33}\mathcal{L}
\end{eqnarray*}$$Because these are boring old differential equations, you may now substitute values for the components of ##\eta^{ij}##. You no longer expect the indices to match, any more than you do when you say something like ##\eta^{22}=-1##.
Your problem is that you substituted in some components of the metric, then expected the result not to be an expression about components.