You need to close the gate for the area. That location has two possible encounters, you must have fought the other one. You will need to get past the Proto-behemoth again as its encounter will also reappear when you close the gate. If you get the wrong encounter again, just jump back off the platform to make it despawn then jump back on to try again.
"Oh, I never leave home without my party cannon!" -Pinkie Pie
Might want to save before fighting it if you intend to also get the crystal. That way you can just reload the save if it doesn't drop its crystal instead of redoing the whole level. If all you care about is the database, no need for this.