The breaking changes are changes in regards to the previous version of the .NET Framework : based on these changes  certain applications and the relative development environments will behave differently from the version 1.0 and 1.1
These are not necessarily changes that will make the applications incompatible or non-functional: they are in fact  different behaviours discovered by Microsoft during design review and debug of tests that could potentially impact the applications. In the current status around 30 situations in which there is an impact on the applications have been identified, for further details consult
The run-time changes can be classified into two categories: The first is an API-breaking change where a function has changed or been removed. In almost all cases these changes have been made due to security reasons. The second, more common type of breaking change is a behaviour-breaking change where the behaviour of a method has changed. 

All known breaking changes in the .NET Framework 2.0 have been reviewed in detail. These breaking changes have been made for a number of reasons, including standards compliance, customer feedback, and correctness. We have attempted to be exhaustive in documenting the changes in the above-mentioned file, but believe that many of these changes will impact very few users.