When opening a new project with existing sources (Such as from a git repository), some files fail to open with the following error window:
When pressing Cancel I get this window:
When pressing Try Again It sometimes works other times I have to force quit and start over. It can take a few tries to finally get the project to open without this error message.
Judging by your commentary, you are probably adding Temp, obj and Library folders to the repository. You can delete those before opening Unity, mainly the Temp folder.
Take a look at the manual: http://docs.unity3d.com/Manual/ExternalVersionControlSystemSupport.html
(The manual fails to explain the Temp folder, since it is deleted when you exit the Editor, but treat it as the Library folder in the steps 4 and 8)
Everything but the Assets and ProjectSettings folders were deleted, so unity had to generate everything else.