I use both version 4.61 and 5.1 on the same computer. When I run my 5.1-project Episerver automatically adds assembly directives to web.config on my 4.61-site. At the same time Vstudio adds web.config to the project. This is very annoying - sure I can remove the directives, but it should not be like this.
This is a known issue and something that is caused by Visual Studio when you got the EPiServer SDK installed. This is considered a Visual Studio problem.