The following example illustrates the problem:
\documentclass{scrbook}
\usepackage{classicthesis}
\begin{document}
\chapter{Test}
\section[String for ToC and header]{This is a very very very long section heading additional technical words}
\end{document}

classicthesis
hass the following settings for section titles (titlesec
is loaded internally):
\titleformat{\section}
{\relax}{\textsc{\MakeTextLowercase{\thesection}}}{1em}{\spacedlowsmallcaps}
If you want to prevent the hyphenation, you can use \raggedright:
\documentclass{scrbook}
\usepackage{classicthesis}
\titleformat{\section}
{\raggedright}{\textsc{\MakeTextLowercase{\thesection}}}{1em}{\spacedlowsmallcaps}
\begin{document}
\chapter{Test}
\section[String for ToC and header]{This is a very very very long section heading additional technical words}
\end{document}

Similar changes will have to be applied to subsections and subsubsections (for chapters this is not needed, since \raggedright
was internally used):
\documentclass{scrbook}
\usepackage{classicthesis}
\titleformat{\section}
{\raggedright}{\textsc{\MakeTextLowercase{\thesection}}}{1em}{\spacedlowsmallcaps}
\titleformat{\subsection}
{\raggedright}{\textsc{\MakeTextLowercase{\thesubsection}}}{1em}{\normalsize\itshape}
\titleformat{\subsubsection}
{\raggedright}{\textsc{\MakeTextLowercase{\thesubsubsection}}}{1em}{\normalsize\itshape}
\begin{document}
\chapter{Test}
\section[String for ToC and header]{This is a very very very long section heading additional technical words}
\end{document}
babel
settings do you use?