The issues that Mt. Gox has been experiencing are due to an unfortunate interaction between Mt. Gox’s implementation of their highly customized wallet software, their customer support procedures, and their unpreparedness for transaction malleability, a technical detail that allows changes to the way transactions are identified.
Transaction malleability has been known about since 2011. In simplest of terms, it is a small window where transaction ID’s can be “renamed” before being confirmed in the blockchain. This is something that cannot be corrected overnight. Therefore, any company dealing with Bitcoin transactions and have coded their own wallet software should responsibly prepare for this possibility and include in their software a way to validate transaction ID’s. Otherwise, it can result in Bitcoin loss and headache for everyone involved.
The Bitcoin core development team has worked to limit transaction malleability. There is broad agreement in the community that this needs to be eliminated. Finding the best and most responsible solution will take time. In the meantime, users of the reference implementation do not need to be concerned. Transactions are always tracked properly by the Bitcoin-Qt/bitcoind software.
This is a good reminder that Bitcoin is still young and experimental. There are best practices to think about and account for by those who want to build companies. To help improve both the reference implementation and third party software, the Foundation is committed to working with companies to produce best practices to help improve software.