How do you get yellow pikmin?

First calm down. O.k. They are not in a hole. Only the purple and white pikmin spawn in holes. There is another special pikmin that spawns in holes but I don't think you have them yet. First of all, you need to have the Perplexing pool level open. As soon as you walk down the slope there, A little scene will play showing you where they are. To get the level open, There is another globe half in awakening wood similar to the one in valley of repose that will open perplexing pool. If you are still stuck in valley of repose then go down the emergence cave and collect the globe half with the purple pikmin in there by tossing pikmin into the purple flowers.

On picmin 2 you will find the yellow unyin in the third level

You need to unlock the perplexing pool. Bring red pikmin to kill the fiery bulborb, then use white pikmin to break the fence, then go call the yellow pikmin. (Be mindful of the snitch bug, and try to kill him with yellow pikmin because they jump the highest.)

After breaking the poison gate in awaking woods and grab the globe with 101 pikmin or 10 purple 1 other then you go to the perplexing pool and you will need to use more white pikmin to get past the wall then call and use them to kill the snitch bug and then you can also get the blue after that just so you know