First of all, if you had trouble finding this Pokémon, you are not alone. In Pokémon Legends: Arceus there are many Pokémon scattered throughout the map and it is not easy to find them all.
Togepi Location | Pokemon Legends Arceus
So where do you start your search of Togepi?
Togepi is a Level 33 Pokémon and is usually located just below Bathers Lagoon, near Hideaway Bay. You can find Togepi somewhere around the water.
My suggestion is if you want to catch Togepi with ease use a smoke bomb.
Throw the smoke bomb so you can get closer to Togepi. When you drop the smoke bomb, you enter the smoke and you can be in short distance from Togepi.
Finally, just throw the Poke ball and catch Togepi!