It is indeed possible to reproduce the described behavior with the svjour3 document class for SPringer journals with the following minimal code
\documentclass[twocolumn]{svjour3}
\usepackage{lipsum}
\begin{document}
\lipsum[1-14]
\end{document}
The highlighting was added manually:

The reason this is occurring is that TeX was not able to meet all the rules for spacing as per the Overfull \hbox messages. One way to fix this is to add \sloppy which relaxes the rules for inter word spacing. See the answers to Why is text being placed beyond the specified line width? for a more detailed explanation.
\documentclass[twocolumn]{svjour3}
\usepackage{lipsum}
\begin{document}\sloppy
\lipsum[1-14]
\end{document}
which yields:

Alternatively, as Marco suggested, you could add \usepackage{microtype} to the preamble. See the microtype package documentation for more details.
If you are not set on justified text, you can use \raggeddright, or \RaggedRight from the ragged2e package.
\documentclass[twocolumn]{svjour3}\usepackage{lipsum}\begin{document}\lipsum[1-9]\end{document}the alignment in the columns are justified. I'm using this version ofsvjour3. Are your alignment issues dealing with poor hyphenation? – Werner Oct 19 '11 at 16:59