This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
The explosion that hurled the Moon across space was magnetic, not atomic in nature; perhaps it affected the quantum field and caused the Moon to slip between normal and hyperspace at random intervals.
In three episodes of the first season ("Black Sun", "Collision Course" and "The Testament of Arkadia") and possibly a fourth ("War Games"), it's either theorized or shown outright that a "cosmic intelligence" had a hand in the original lunar explosion and the Alphans' later travels.