Why i don't have the bar over the letter R?

Use \bar for short lines and \overline for longer lines.

A separate comment: In fine math typography, a \cdot is generally preferred over * to denote multiplication.

\documentclass[11pt]{report}
\usepackage[utf8]{inputenc}
\usepackage{mathtools,array}
\begin{document}

\begin{align*}
C_f 
&= 100 - 100\cdot\frac{\overline{R_{j(pr)}}}{\overline{R_{j(obs)}}} \\
&= 100 - 100\cdot\frac{\bar{R}_{j(pr)}}{\bar{R}_{j(obs)}}
\end{align*}
\end{document}

Like this? Then you just messed around with the curly brackets. (Edited the over-frac-issue)

\documentclass[11pt]{report}
\usepackage[utf8]{inputenc}

\usepackage{mathtools,array,dcolumn}

\begin{document}

\begin{equation}
Cf = 100 - (100* \frac{\bar{R}_{j(pr)}}{\bar{R}_{j(obs)}})  
\end{equation}

\end{document}

When using the bar-command the following brackets include the barred content. Because you just wanted the 'R' to be barred - only include the R into the brackets.

Apply the command only to R. However, I would use the\widebar\ command, from mathabx, without loading the package.

I added some other improvements: bigger parentheses, and pr and obs typed as text, not as the products of variables:

\documentclass[11pt]{report}
\usepackage[utf8]{inputenc}
\usepackage{amssymb}
\usepackage{mathtools,array,dcolumn}

\DeclareFontFamily{U}{mathx}{\hyphenchar\font45}
\DeclareFontShape{U}{mathx}{m}{n}{
<-6> mathx5 <6-7> mathx6 <7-8> mathx7
<8-9> mathx8 <9-10> mathx9
<10-12> mathx10 <12-> mathx12
}{}
\DeclareSymbolFont{mathx}{U}{mathx}{m}{n}
\DeclareFontSubstitution{U}{mathx}{m}{n}
\DeclareMathAccent{\widebar}{0}{mathx}{"73}

\begin{document}

\begin{equation}
C_f = 100 -\biggl (100* {\widebar{R}_{j(\text{pr})}\over{\widebar{R}_{j(\text{obs})}}}\biggr)
\end{equation}

\end{document}