Everything in the universe is such a broad word.
One thing that QM does not deal with is for example gravity. There are attempts to apply QM on gravity, but they are not successful so far and as it stands, QM cannot be applied here.
There is also problem with applying QM to everything at once. QM is quite problematic when it comes to explaining measurement. The standard formulation of QM introduces special agent to deal with it. So you need something outside of your QM system to act as this agent, which contradicts your attempt to apply QM on everything.
You may say, that QM should apply to everything as it is according to our understanding most fundamental theory we have, but that does not mean it does. Existence of quantum gravity might look promising, but we do not know yet. The measurement problem is however quite different and there is less hope it will be solved withing the framework of QM. It can be dodged as long as you retain some external agent - which is the strategy physicists adopted - but as long as you want to include everything there arises a problem. I think (I heard Lee Smolin to talk about it somewhere) research in quantum cosmology faces just this problem.
I would like to explain better the use of my word "agent". The problem is, that somewhere in the transition from QM to classical, the system must make choice about its state. The problem is QM does not define when does this happens, only how does this happens. It is up to the physicist to know when to apply the collapse during calculation, QM itself does not dictate this. The collapse itself is integral part of the QM, but when it happens is not. This missing knowledge that is left upon the physicist making the calculation makes QM not self contained and therefore it cannot be applied on "everything" in this sense. The choice must be made outside of its realm.
But of course this is based on standard formulation of QM I was taught. I do not follow research on this topic, so if there is more knowledge about this problematic, I would be glad to be corrected and read more about this. However, I remember from book by Sabin Hossenfelder "Lost in Math" that measurement problem is still huge hole in QM.