Currently I'm compiling and loading an assembly at runtime. The assembly contains always the same namespaces and classes. When I'm doing this multiple times in the same application instance, does always the newest assembly will be used, when creating new instances of the classes which are in the assembly? Or is this not guaranteed?
You're creating exactly what you're trying to create. This may or may not be what you want to create, though.
Most likely, your assemblies don't have a specific name, but rather, a randomized unique name - in that case, the types are entirely different and only accidentally similar as far as .NET is concerned. Types from two different compilations are entirely unrelated, and are not compatible. This may or may not be a problem when you're accessing them through an interface defined outside of the dynamic assembly, depending on how exactly you're using the types.
If you add an assembly name, the situation gets a bit more complicated. You can't load the same assembly twice (the old one is not replaced by the new one), so you need to change the version. However, two versions of the same assembly cannot be loaded in the same application domain (except when doing "fun" with AssemblyResolve etc. - but that's quite tricky to get right). The second assembly would simply fail to load.
In the end, the Type you're trying to instantiate is the one you do instantiate (barring the use of binding redirects, which are bonus fun :P). If some piece of your code holds on to a Type from a previous compilation, that's what it's going to create.