It looks like you might have correctly added those repos as submodules but you've changed/added/deleted a file inside those repos. If you cd into bundle/nerdtree and do a 'git status' it should tell you what is different. If you get the submodule back into a clean state the top-level one should stop saying "modified content"
Also, your command:
git submodule add bundle/YouCompleteMe/
is incorrect. 'git submodule add' takes a repo url like so:
git submodule add https://github.com/Valloric/YouCompleteMe.git
But from your output it looks like you've already done that correctly at some point. You appear to be using Pathogen to manage your submodules - the docs for it should walk you through this process pretty well. Or you could switch to Vundle which apparently has some advantages (personally I'm still on Pathogen).