Let $\mathbb{R}=(\{\textrm{real numbers}\};0,1,+,\times)$. Is there an equivalence relation $E$ on $\mathbb{R}$ such that $\mathbb{P}_\mathbb{R}(E)$ is not upwards-directed?
I will assume that the order on $\mathbb{P}_\mathbb{R}(E)$
is the inclusion order. If that is what is meant, then the answer
to the question is Yes, there is such an equivalence relation.
Let $E$ be the equivalence relation on $\mathbb R$
whose classes are $A=(-\infty,0]$ and $B=(0,\infty)$.
Let $f\colon \mathbb R\to \mathbb R$ be the $E$-transversal
for which $f(A)=\{0\}$ and $f(B)=\{1\}$.
$\mathbb R_f$ is a $2$-element algebra and
the operation tables for ${\mathbb R}_f$ are
$$
0^{{\mathbb R}_f} = 0, \quad
1^{{\mathbb R}_f} = 1, \quad
\begin{array}{|c||c|c|}
\hline
+ & 0 & 1 \\
\hline
\hline
0 & 0 & 1\\
\hline
1 & 1 & 1\\
\hline
\end{array}, \quad
\begin{array}{|c||c|c|}
\hline
\cdot & 0 & 1 \\
\hline
\hline
0 & 0 & 0\\
\hline
1 & 0 & 1\\
\hline
\end{array}.
$$
Now let $g\colon \mathbb R\to \mathbb R$ be the $E$-transversal
for which $g(A)=\{-1\}$ and $g(B)=\{1\}$.
$\mathbb R_g$ is a $2$-element algebra
and the operation tables for ${\mathbb R}_g$ are
$$
0^{{\mathbb R}_g} = -1, \quad
1^{{\mathbb R}_g} = \hphantom{-}1, \quad
\begin{array}{|c||c|c|}
\hline
+ & -1 & \hphantom{-}1 \\
\hline
\hline
-1 & -1 & -1\\
\hline
\hphantom{-}1 & -1 & \hphantom{-}1\\
\hline
\end{array}, \quad
\begin{array}{|c||c|c|}
\hline
\cdot & -1 & \hphantom{-}1 \\
\hline
\hline
-1 & \hphantom{-}1 & -1\\
\hline
\hphantom{-}1 & -1 & \hphantom{-}1\\
\hline
\end{array}.
$$
If $\mathbb{P}_\mathbb{R}(E)$ were up-directed by inclusion,
then there would exist an $E$-transversal
$h\colon \mathbb R\to \mathbb R$ such that
$\textit{Th}_{\textrm{Eq}}(\mathbb{R}_f)\cup
\textit{Th}_{\textrm{Eq}}(\mathbb{R}_g)\subseteq
\textit{Th}_{\textrm{Eq}}(\mathbb{R}_h)$.
There are many ways to see that there no such $h$.
The easiest might be this:
$0^{{\mathbb R}_f}$ is a neutral element for $+^{{\mathbb R}_f}$
and $0^{{\mathbb R}_g}$ is an absorbing element for
$+^{{\mathbb R}_g}$. If
$\textit{Th}_{\textrm{Eq}}(\mathbb{R}_f)\cup
\textit{Th}_{\textrm{Eq}}(\mathbb{R}_g)\subseteq
\textit{Th}_{\textrm{Eq}}(\mathbb{R}_h)$
then $0^{{\mathbb R}_h}$ would be both
a neutral element and an absorbing element for
$+^{{\mathbb R}_h}$. This leads to a deduction
$$
x\stackrel{neut.}{\approx} (x+0) \stackrel{abs.}{\approx} (y+0)
\stackrel{neut.}{\approx} y,
$$
or $x\approx y$ in $\textit{Th}_{\textrm{Eq}}(\mathbb{R}_h)$.
But this is impossible, since
$\mathbb{R}_h$ must be a $2$-element algebra
if $h$ is a transversal for an equivalence relation with $2$ classes.