That is the usual behavior. The first number reflects the section number, in this case. The second number counts the occurrence of a definition within a section.
This means that the first definition in the second section would be: Definition 2.1.
The third definition in section 4 would be: Definition 4.3.
What you want to get, if I understood you correctly, you get by
- removing the square bracket in
\newtheorem{definition}{Definition}[section]
- and resetting the
counter before each definition:
\setcounter{definition}{0}
Your code would look like this for the definition in section 2:
\newtheorem{definition}{Definition}
\setcounter{definition}{1} % sets counter to one, next definition starts with 2
\begin{definition}(Definition.){
Eine Definition ist die Bestimmung eines Begriffs}
\end{definition}
Note, however, that if you have more than two definitions in a section, you will get trouble with this numbering.