Welcome to words. We use words this way =)
Actually, what you hit on is a rather fundamental and interesting detail. Even in philosophy, we must define the "domain of discourse," which is that which can be discussed in the discussion. Informally, it defines what "everything" is for the purposes of talking about it.
In the case of the "Theory of Everything" in physics:
A theory of everything (ToE), final theory, ultimate theory, or master theory is a hypothetical single, all-encompassing, coherent theoretical framework of physics that fully explains and links together all physical aspects of the universe.
Given that the domain of discourse for physics is... well... physical aspects of the universe, their usage of the word "everything" is reasonable. Of course, it doesn't qualify as "everything" in other discussions. Even within physics, the ToE explicitly does not include the initial state of systems, merely the eternal rules governing it. But within the community it is well understood.
To hold physics to a stricter standard than that would be tricky. Consider, for example, the Tao, which could be loosely translated as the Chinese concept of "everything." The famous quote about the Tao is:
The Tao that can be expressed is not the eternal Tao.
Well that's a bugger. If you are discussing "everything" in a scope which includes the Chinese concept of the Tao, you actually can't express everything!
Beyond that, there's a pragmatic reality: the catchy terms are the ones that stick. The whole big deal about the ToE is that, right now, our standard model has a symmetry group of SU(3)xSU(2)xU(1), which is just... messsy, by physicist standards. A ToE would unify that into one group, and that is desirable by physicists (for whatever reasons they wish to state). However, "Theory unifying SU(3)xSU(2)xU(1) into a single simple symmetry group" just doesn't quite have the market appeal as "Theory of Everything." That's how marketing works.
On a related note, Philosophy's etymology comes from "the love of knowledge." However, I can guarantee you that there are philosophers out there that don't truly love knowledge. That's just how people are. Do we need to relabel them because "philosopher" is a misnomer for them?