Yes! You can also catch Pokémon at Emera Beach by fishing them up
and in the Safari Zone! You can "catch" certain Pokémon as an egg
as well in the Tall Grass, special Rumble areas, the Royal Tunnel,
the Ancient Cave, and buy them from the Gem Collector with gems if
you have the Pokedex entry for that Pokémon. The Honey Tree is the
only area that I'm aware of where you use your own Pokeballs from
your item bag, though!
@iheartkatamari In addition to what has already been said, there is
also the shadow radar, that you need Pokeballs to 'catch' shadow
mons, which can be bought at the item shop for 500k PD. Also, in a
way, most things on this site could be thought of as 'catching'
Pokemon. Eg. adopting lab eggs, game center, bug hatching contest,
daycare, SCS, the fun fair event
Combee can be caught at the honeytree, bred in the daycare, or
bought from other players. Also, next time, it would be better if
you create a new thread, instead of posting in a partially