Philosophy is less in the business of showing when a theory is false, or when premises in a theory are unsound, and more in the business of showing when a theory is shallow, or when the inferences from a theory's premises are invalid. Socrates did not prove to Euthyphro that polytheological voluntarism is wrong per se, but that Euthyphro's understanding of his own commitment to that ethical system was unrefined, even inchoate (such as by lending itself to inconsistencies that Euthyphro did not appreciate beforehand). And so it went in many of Plato's dialogues over general definitions of concepts/terms.
Now, with respect to the science/pseudoscience distinction, we have to differentiate between something that is merely not scientific, and something that is actively pretending to be scientific. Perhaps this distinction will itself prove futile to try drawing with sharp lines, but for now:
The phrases “demarcation of science” and “demarcation of science from pseudoscience” are often used interchangeably, and many authors seem to have regarded them as equal in meaning. In their view, the task of drawing the outer boundaries of science is essentially the same as that of drawing the boundary between science and pseudoscience.
This picture is oversimplified. All non-science is not pseudoscience, and science has non-trivial borders to other non-scientific phenomena, such as metaphysics, religion, and various types of non-scientific systematized knowledge. (Mahner (2007, 548) proposed the term “parascience” to cover non-scientific practices that are not pseudoscientific.) Science also has the internal demarcation problem of distinguishing between good and bad science.
A comparison of the negated terms related to science can contribute to clarifying the conceptual distinctions. “Unscientific” is a narrower concept than “non-scientific” (not scientific), since the former but not the latter term implies some form of contradiction or conflict with science. “Pseudoscientific” is in its turn a narrower concept than “unscientific”. The latter term differs from the former in covering inadvertent mismeasurements and miscalculations and other forms of bad science performed by scientists who are recognized as trying but failing to produce good science.
Pretense as a means of going around a public/intersubjective commitment to factual representation, as a potential subversion of this representation, appears to involve a problem of social ethics, then. Depending on how wide one takes the intersection of ethical theorizing and philosophy to be, then, one might count an ethical judgment of the Time Cube theory as somehow philosophical. So take the snippet of the original site, as copied to Wikipedia's article on the topic:

We have Ray characterizing the normal education system as evil, and not just in general (which is not so unbelievable), but on account of implicit or explicit rejection of, and dissociation from, Ray's theory. Not only that, but he floats the idea of killing educators for their refusal/failure to promote his theory. His confidence in the merits of his theory is utterly self-absorbed, borderline solipsistic, in the first place.
So even before we judge the Time Cube theory to be pseudoscience, we can actually go ahead and judge it to be pseudophilosophy, since he makes implicit epistemological, metaphysical, and axiological/deontological judgments that conflict with the spirit of philosophy (in which arrogance has little to no place). Or if not that, then antiphilosophy first, pseudoscience second (or besides). And then since the Time Cube theory tries to ground itself in opposition to peer-reviewed consideration (with a hostile sealioning-like claim at the end of the quoted section from Ray's site), evades mathematical clarification/specification, and all that in the service of a theory that itself is little more than triviality or poetry (or both), that is where it betrays its identity as pseudoscience most precisely, even for a philosophical reason: in a sense, "of course" we can represent some of the flow of time around a sphere with a cubic pattern. In fact, it was just recently discovered that the general theory of cubes is able to help us better interpret the theory of black hole formation:
One of Schoen and Yau’s major innovations was to recognize that an equation devised by the physicist Pong Soo Jang, which originally had nothing to do with black holes, can “blow up” — go to infinity — at certain points in space. Amazingly, where it blows up coincides with the location of a closed trapped surface. So if you want to find such a surface, first figure out where the Jang equation goes to infinity. ... Hirsch, Kazaras, Khuri and Zhang also rely on the Jang equation. But in addition to a torus, they use a cube — one that can be seriously deformed. This approach “is akin to Thorne’s idea, using square hoops instead of traditional circular hoops,” Khuri said. It draws upon the “cube inequality” developed by the mathematician Mikhail Gromov. This relationship connects the size of a cube to the curvature of space in and around it.
Again, then, it's less that the Time Cube theory is false, or can be philosophically demonstrated to be false, and more that the theory is both unethical (in the way of Ray's presentation) and superficial (reading more into the obvious cube-theoretic structure that can be read into the target context (time) than is valid to infer from that structure (as if we were to take e.g. Aristotle's square of opposition and try to directly infer that existence itself is arranged uniformly, primarily, and/or only in a square-like manner, as some sort of "Space Square" (if you will))).
Condensed argument:
- Meaning is, in part, socially grounded; or at least must be so grounded when the "faculty" of semantics is used publicly.
- An antisocial presentation of a theory is not properly socially grounded: either the proponent tries to mean their own thing by their words and the socially intended sense/referent of those words (so the theory's semantics is overloaded), or they are pretending that their personal definitions are the public ones and equivocally criticizing public apathy or opposition to the theory based on those definitions (and the theory has an oscillating semantic deficit).
- Not, then, that the antisocial theorist (e.g. Ray) is even trying much to convince people that their theory is itself true, but that such a theorist is casting a wide net, trying to rope in those gullible enough to be mesmerized by their poetry. The cognitive predator is not aiming at truth, as such, at all, but is looking for cognitive prey, for people who they can use poetry on to get emotional support from. (We might also speak of cognitive parasites, though Ray's overtly violent rhetoric mirrors predatory rather than parasitic behavior.)