A little care should be taken when version controlling a 2D Toolkit project. It is advisible to use text version control in Unity where possible - it is much easier to identify and fix issues that way.
Always exclude these files from version control. These files contain editor assets, and runtime-loadable assets - all of which can be reconstructed by invoking "2D Toolkit > Rebuild Index".
After updating / getting latest version from version control, make sure to "Rebuild Index". This will rebuild the index and update any necessary runtime files.