mutare is an infinitive in latin. we have infinitives in english too: 'to drive', 'to walk', 'to read', etc., basically the most simple form of a verb. we call them infinitives because this form of the verb has the most possibilities, it is not tied down to any specific subject (verb-er) object (verb-ee) or tense (past, present, future, etc.)
in order to assign a verb to a particular noun, we have to add some signifiers of which noun it belongs to. in english, we remove the 'to', and for singular subjects we usually add 's' at the end (she drives, she walks, she reads, etc.). in latin it's a little more complicated, but it's the same general principle.
the grammar of mutare materia is wrong because it is trying to assign an infinitive (which, by definition, shouldn't be assigned to anything except in specific circumstances) to a noun, without going through the proper channels of adding signifiers. mutare materia means 'to change matter', and it gives no indication of whether something is changing the matter, whether the matter is changing something else, or whether the matter itself is changing.
what i suspect it intends to say is 'changing matter', i.e. matter that is itself in a state of changing. this form of a verb is called a participle, which functions as a sort of adjective made out of a verb to describe a noun. in latin, this would be mutans materia.
latin unfortunately doesn't have a present passive participle, so if we wanted to say 'matter being changed' we would have to instead say something like 'matter which is being changed': materia quae mutatur, which just isn't quite as catchy.
i'm pretty sure a participle would be the best form to use because the term mutare materia presents itself in opposition to prima materia (meaning 'first matter'), in which prima is an adjective describing materia, just as mutans would be a sort of adjective describing materia.
from what i have gathered about my (brief) research on prima materia, it is a term in philosophy and alchemy which describes a sort of substance which is the basis for all things, an elementary matter which is necessary for the creation of the philosopher's stone. i think it's basically what all stuff is made out of.
mutare materia, as far as my google searches have revealed, is entirely a magnus protocol creation, seeing as the only thing i found on it was a reddit post discussing an episode in which the term had come up. hence i felt i had the authority to come on tumblr and say that the term isn't great grammatically.
on top of all this, of course, adjectives and participles in latin tend to go after the noun, unless they are deliberately misplaced for emphasis, so you could also argue that it should be materia mutans, and that prima materia isn't great latin.
either way it's a little too late to change it now and i'm sure it's not bothering that many people. but if anyone has an explanation as to why an infinitive should be used PLEASE come tell me otherwise i'll start thinking about grammar every time this term appears in the podcast lol
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