@Melanie983 "It was more that he seemed to think the whole flat was his and he could do what he liked".
You offer full kitchen and living room access. You can't then be miffed that a guest takes you up on that.
What you need to do is to sit down with this guest over a cup of tea and have a chat with him about the expectations when home-sharing, as well as how things work differently in your culture and location than in his.
Tell him that the sewer system and house plumbing where you live is built to handle flushing toilet paper and that is what everyone does and what you would like him to please do. Say you realize that it may seem strange to him, and take awhile to get used to, just as it would seem strange to you to put the paper in the basket if you went to his country, but that you would have to adjust your habits to a different culture.
Explain that you are sharing your home with him and that he needs to respect that it isn't okay to cover the kitchen with his own stuff- that you need to be able to also use your kitchen. Arrange a place where he can store his own kitchen gear- i.e. one of the cupboards that is for him. And if he has redundant things that you already have, like a blender, or cooking utensils, he should box those things up and store them in his room- it isn't necessary for the kitchen to be cluttered up with 2 of everything when guests are allowed to use yours.
And if he isn't cleaning up after himself in the kitchen, make sure to let him know that is necessary- that you are his host, not his personal maid.
Hopefully you can work things out with him with a bit of friendly explanation, as long as there isn't a huge language barrier.