For some reason, when I load up my mod some of the focuses dont appear. Did we do something wrong when making the focuses? 

There is possibly an error in your focus tree; when the game encounters an error it will stop loading the focus tree at the point of the error - even if the rest of the tree is fine.

You can find out what the error is by running the game in debug mode.

If you don't understand what the error is by what's shown in the error log, upload it here and I'll have a look for you: