Only a few minor problem I'm aware of. A new C# project created in VS2010 will have a dependency on Microsoft.CSharp.dll, the runtime support assembly for the new "dynamic" keyword. When you change the target framework version to 3.5, you'll get a warning about this assembly, you have to remove it by hand.
Also, your code will be compiled by the new C# 4.0 compiler, even if you target an earlier version of the framework. That could be the source of a compat problem, code that compiles differently with the 3.0 compiler. The more common compat issue is code that shouldn't compile in 3.0 but did because of a compiler bug. Not a real problem of course, but could byte if you check in code that was written by team members that still use 3.0
You can force the compiler to verify that no new 4.0 features are used accidentally with Project + Properties, Build tab, scroll down/right, Advanced, Language Version = "C# 3.0".
If you want to be sure then wait another couple of months and keep an eye on the feedback at connect.microsoft.com.