I have not had this problem, personally, but I've only just begun using 2012 in the last month.
It is possible that one of the standard MATLAB funciton you're using either
a) has stopped being supported, so it's no longer vetted to see if it works after changing possible dependencies and core MATLAB code.
b) has been changed in a way that the inputs and/or outputs are expected differently.
You're going to have to either track the bug (which sometimes ends up being a can of worms, depending on how complex your code is) or stick with 2011.
In the editor under the (tools, I think) menu, there's a "dependency report". You can use that to see all the functions your program relies on (and can do the same for each of those functions). Then you can check on support for each of those functions in 2012.
here's the release notes. You can click on each topic to expand it and see details on function/handling changes, etc.:
http://www.mathworks.com/help/matlab/release-notes.html