Lucky for us, we get our info about the title straight from the horse's mouth when Jason2 references the concept of "dark matter" while eating dinner with Daniela. Check it:
"Most astrophysicists believe that the force holding stars and galaxies together [...] comes from a theoretical substance we can't measure or observe directly. Something they call dark matter. [...] Some string theorists think it might be a clue to the existence of the multiverse." (6.51-55)
In other words, the title Dark Matter is a reference to the magical glue that holds together the multiverse. There you go, folks.
We'd be lying, though, if we said that this was some complex, hyper-referential title. We mean, yeah, it kind of is, but Dark Matter is just one of those phrases that sounds cool, you know?