The simple answer to this question is *.* , basically it's completely safe to ignore anything you don't want to add to version control. That being said it really depends on what you're looking to accomplish by using Git. If you want to be able to checkout/import your project elsewhere from the same repository then you'll want to ignore at most /bin/. and /gen/., I wouldn't ignore the folders themselves (i.e. /bin, /gen) just for the sake of maintaining the proper directory structure for your project.
That answers the initial question, but is unrelated to the problem you are having. As far as solving the problem you are experiencing is concerned you would have to post more info, specifically what's listed in the Problems tab. If you can't see the Problems tab anywhere then click on the Window menu, then show view, then choose problems if it's there or click on other and look under General to find it.