The events of Prodigy largely involved wormholes across spacetime in one universe (and incursions into that universe by bad guys).

The quantum fissures in Lower Decks are connected to other universes. While this season of Lower Decks does canonically occur in the same time period as season 2 of Prodigy, I doubt the two are related.

That said, with the specific call-out, I definitely see them having some significance later in the season.

I was more surprised that the crew of the other Cerritos weren’t responsible for opening the fissure in the first place. The setup felt like it was leading toward a reveal that Captain Becky’s crew had ulterior motives.

It was a bit disappointing that the twist only turned out to be Captain Becky opportunistically trying to swap universes. I was expecting something more like Stargate SG-1 9x13 (Ripple Effect) wherein an alternate-reality SG-1 is after me Lucky Charms a ZPM.