Basically the title, It says I am in an ocean biome, but a Extreme Hills was generated
http://i.imgur.com/TLLE9Cr.png

Maybe you have made the ocean to look like Extreme Hills, but it still has the ocean biome id.

Does this also happen with the default settings?

Random thing I noticed in your config: you are replacing resources with air. It is much better to remove the resource althogether in the resources queue.

I don't think I did. http://pastebin.com/7ukHvQdY
I also had a similar problem where a plains biome would be listed as a desert, which made all of the dirt to change to sand and stone to sandstone (I added a replace that would change grass to sand so not that big of a deal). It isn't really specific to any biome, in general the biomes weren't synced with the land

here is my WorldConfig for the world if it makes a difference
http://pastebin.com/gfwfAX5R
EDIT: should also mention that when I do //regen the terrain with worldedit it the terrain does not change into an ocean. (doesn't change at all)

Why did you close the issue? Is it solved?

normal config is matches biomes fine, thanks for the resource tip! I will try that out.

no sorry, must have clicked close and and comment instead of just comment
This happened when I was testing more config options XD
http://i.imgur.com/Losx0RP.jpg

So as for the first issue, the real question is, if you change settings of the ocean biome drastically and use //regen or something like that, does the terrain change? Because if you ask me that looks nothing like extreme hills, more likely that your height value is too high. I'm guessing you use worldheight 8 and didn't adjust the heights correctly - reference: https://github.com/Wickth/TerrainControl/wiki/World-Height
So right here I don't see an error with TC, but I don't know about the other things you mentioned (plains listed as desert), but I don't think it's a bug, more likely some weird config error that happened somewhere. But if you give more info we'll find out.

For the second pic, did you change the IsleInBiome value in the mushroom island config? Or is the surrounding biome "ocean"?

Surrounding biome i just ocean for mushroom, should I link a DL to my TerrainControl folder?
I do have the worldheight set to 8, but I don't think that is it because it looks like an extreme hills is generated, I also an trying to get the oceans to be as small as possible

Change the ocean biome values according to the wiki link above.
Your water level is 63, your biome height -1.0. The handy chart in the wiki article shows that biome height -1 will give you an approximate land height of 95 blocks, which is above 63 (your water level). So you can't possibly get any proper oceans with these settings. Try biome height -2.5 or something like that (not -2,0 - it is bugged somehow) and maybe increaste the water level. Then we'll see if that was the issue.

Yup, something still wrong
http://imgur.com/a/OnPwJ#0
Here are my Terrain control files if it helps
http://www.mediafire.com/download/73ik5yn2au3dd1i/TerrainControl.rar
The only real issue with it is the replacing blocks feature

Thank you I think it worked! I set it to -1.99, not to adjust everything else in proportion
EDIT: reopened because there still might an issue with terrain generation/biome match up somewhere
http://imgur.com/a/fJ13P first image is the old pic, last 2 are new with the ocean biome hieght at -1.99. Second pic might be becasue of 99% land rarity

I'll try it tomorrow. For the forest that looks like a desert, does it
also return forest if you type /tc biome? You did restart the server and
delete the region files after changing the config, right?

It just got a little weirder, it said /tc biome said extreme hills. This was the first time the map was loaded on the server (this was my real server not test). I usually delete the file or /mv delete the map and restart. I didn't necessarily restart, but the server crashed a few times due to an unrelated issue in between me changing the configs and loading the maps, so I guess yes the server did restart (complete stop and start up).

I should also mention that for the map Terrain WorldHeightBits is set to 8 and water level 94. For Test WorldHeightBits is 7 and water level is default (63).

Not sure, but I think the problem is caused by having landrarity higher than 97%