Some of the balls added in 3.3Beta will cause the game to crash if you add a Pokemon caught with one to your party. Any subsequent time you try to log in the bug occurs again and the game crashes. Thankfully, the devs fixed this quickly enough. Sadly, we won't see the bugfix until the next release. If you are like me, you don't want to wait until the next release to play then rejoice! I've found a solution to the problem. However, it is not without it's risks, it requires modifying save data. Please backup minecraft before attempting, I am not responsible for any damage this may cause. Use at your own risk!
Edit: To clarify, the new pokeballs UI textures are failing to load, causing the game to crash. This tutorial will teach you how to switch out what pokeball your pokemon was caught with to an ultraball. This way when the game loads it will just load an ultraball texture instead of crashing. This is simply a work around. The issue itself will be fixed in the coming version.
I'm going to assume you are using Windows, but the principles are the same on Linux and OSX. If you are on a local game follow the directions below, this works on a server as well but you need to have access to the servers world data.
1) Step one, open up your minecraft folder. This can be done by hitting start, typing in %appdata% and hitting enter. You will see a folder titled .minecraft you might have to enable show hidden files to see it.
2) Open up the saves folder, then open up your world folder, then open up the pokemon folder.
3) If you are in the right place you should see some files that end in '.pk' and '.comp'. The '.comp 'files represent the pokemon in a players PC and the '.pk' are the pokemon in a players party. The numbers of the file name represent the players ID, so if you are modifying server files you will have to know the players UUID or just open them up in a text editor and search for the player name.
4) Copy your .pk file to somewhere easy to find like your desktop.
4) You'll need a hex editor for this next step. A hex editor is a program that allows you to view and modify the data in a file. There's a safe and free one for Windows called HexEdit that can be found at http://www.hexedit.com/ . You can use any hex editor though.
5) Open up HexEdit and open up your .pk file you copied to your desktop. You should see a ton of really weird looking data on the left (hexadecimal, or hex for short) , and on the right you might be able to see a few english words with some gibberish thrown in (ASCII, or plain-text).
6) Hit crtl-f and type in the name of the pokemon you caught with a glitched ball then hit enter. This should bring you to the part of the file you need. Look at the block of ASCII (english like stuff) on the right, you want to find the text 'CaughtBall' between the two occurances of your pokemons name. Here's an example, , I searched for Zapdos:
....stuff you don't care about....
...more stuff you don't care about...
7) Between CaughtBall and PixelmonMovePP3 there should be 7 periods. Highlight them, DO NOT HIGHLIGHT ANYTHING ELSE
8) See the data on the left that got highlighted too? Thats the datavalue for the ball, lets replace it with an ultra ball. Right click over the data, and select allow changes. Right click again, make sure insert is not selected.
9) Then replace the highlighted data with
00 00 00 02 03 00 0F
You should only have to change one or two of the fields. Click before the field you want and push 3 if you want to fill 03, or 2 if you want to fill 02. Make sure you don't add any data or remove any data! Make sure there are only 7 periods between caughtball and the next data field.
9) Save the file and put it back in your .minecraft folder where you found it, crack open a beer and enjoy!
I'm currently working on writing an application to do this for you as well as easily make other modifications to you pokemon so you won't have to modify the file yourself. However, with school and work it will probably be a couple of weeks.
Let me know if you have any questions and good luck!