But weren't the Gems already trying to find them?

In fact… What happened to that? They just kind of… abandon that whole plot point of Malachite being dangerous. I suppose they're now worrying about the Cluster, but it seems like they completely forgot the ticking time-bomb in the ocean.

I haven't gone back to watch those episodes, but I'm sure the Gems had been super busy looking for Peri and Malachite up until Peri took residence in the bathroom.
After that the ticking time-bomb in the center of the earth became a priority.