There are different opinions but most people don't think it was a engineering problem. From the beginning the project had three responsible managers with different interests: Klaus Wowereit (Governing Mayor of Berlin), Matthias Platzeck (Minister-President of Brandenburg) and Meinhard von Gerkan (famous Architect).

Meinhard von Gerkan published a book about the project, offering his view: Blackbox BER [1]

[1] http://www.amazon.de/Black-Box-BER-Brandenburg-Gro%C3%9Fbaus...