Geometrical transformations (see example) break the fitting of node sizes. This used to work in older releases (I checked it with an installation of Xubuntu 10.10, which brings pgf 2.00) but does not work anymore with kubuntu 17.10 (pgf 3.0.1a).
I think what happens is that the enclosing node is fitted in transformed coordinate space (instead of the original one), and that then the coordinate transformation applied once agaon.
\documentclass[tikz]{standalone}
\usepackage{tikz}
\usetikzlibrary{scopes,fit,backgrounds}
\begin{document}
\begin{tikzpicture}[scale=1,transform shape]
\tikzstyle{tA}=[draw,fill=red!10!yellow]
\tikzstyle{tB}=[draw,fill=red!30!yellow]
\tikzstyle{geom}=[xslant=1.5,yscale=0.5,rotate=0]
\begin{scope}[geom]
\node[tA] (n1) at (0,0) {A};
\node[tB] (n2) at (0,1) {A};
\node[tA] (n3) at (1,0) {A};
\node[tB] (n4) at (1,1) {A};
\node[fit=(n1) (n2), draw] {x};
\draw[blue,->] (n1.south) -- (n1.north); \draw[blue,->] (n2.south) -- (n2.north);
\end{scope}
\end{tikzpicture}
\end{document}
Here the result from pgf 2.00 with the same code (which I think is what it should be).