“That’s the last time we go surfing on your back,
Croconaw!” she shouted angrily, pointing a damp wing towards him.
Add a comma after "back."
Looking more closely, he could see that the clouds were gradually moving to the east, back to from where they had come
, towards the village.
Bold part seems awkward. Try "back to where they had come from."
“It’s not my fault we ran into rough water by the end of it. This is called 'Stormy Sea'
, for a reason.”
Croconaw's sentence is in the first set of quotation marks, so something he quotes (In this example, the name "Stormy Sea") should be in apostrophes.
There weren't very many errors besides those until you get closer to the end, so I'll skip ahead a little.
Tristan turned to peak around the rock for a second time....
...The other Pokemon, who was farthest away from them, was a deep blue coloured fish with long yellow whiskers and yellow shaped “w” on his forehead.
These were in the same paragraph, so I put them together. "Peak" is synonymous to "summit", while "peek" means to look. You meant "peek" here but put an "a" in by mistake, something a spell-check wouldn't pick up.
Also, the description of Whiscash could use some work. "Yellow shaped 'w'" is my main point here; yellow's not a shape!
Try "A yellow 'W' shape on his forehead"
Tristan rolled his eyes. Why did everyone have to make such a big deal out of this simple expression. He didn’t use it that often.
Three periods in a row, and all three could be replaced with something else to give these sentences a bit more life. Give this a shot:
Tristan rolled his eyes; why did everyone have to make such a big deal out of this simple expression? He didn’t use it that often...
The ellipses at the end isn't necessary, but the other two punctuation marks would definitely help.
“Ah! So you are Team Supernova! The team that I’ve been hearing so much about!” the old fish exclaimed. “Finally, I get the chance to meet you! I’ve heard so many good things about you from Plusle, Caterpie, and especially Minun!”
A bit of overuse of exclamation points here. Again, trade a few of them out for question marks and whatnot.
"Ah... So you are Team Supernova, the team that I've been hearing so much about!"
That should be enough
Imagine my horror when the entire village fell into the sea! Never did I imagine that something like that would ever happen!
You left out the quotation mark at the end, and the exclamation point there doesn't seem to fit. Try an ellipsis instead.
“Okay...?” Tochic replied slowly. “What’re we gonna do about it then?”
“Well-” Croconaw said before being cut off.
Tristan stepped forward so that he was directly in front of the rock in question. “Whoever’s back there!” he stated. “You have to the count of five before we beat the crap out of you!”
Nothing wrong here, I just like this part
Both of his team mates jaws dropped in disbelief, but the threat had done his trick.
Add an apostrophe at the end of "mates" to make it possessive, and change "his" to "its."
How many more villagers were still wandering amongst the rocks.
Needs a question mark.
“You don’t have more of those
do you?” Torchic asked curiously.
“Only a few,” Whiscash answered. “I think now would be an appropriate time to use it
Add commas after the bold words.
I’m not gonna turn around after all this?
I don't think Torchic is asking a question. She seems pretty sure of herself. :P
Well, that should do it. I think I missed a few, but now that you know what to look for I'm sure you can find them yourself.