You are getting this because there is a conflicting dependency somewhere. For example, if you have plugin A that depends on dependency.X-1.0.0 installed, and try to install plugin B that depends on dependency.X-1.1.0, there is a conflict. When you check for updates, Eclipse will check all plugins and features you have installed in the past.
Try to update one thing at a time to identify which update has a conflicting dependency.