Creating a site, selecting all the tools and the next page ask you for information for some of the tools (screenshot1). On that page, without filling anything, press the back button (screenshot2). Then the tools where you didn't fill any parameter are not in the list now (screenshot3). If you continue again to the next page and all the options to fill the parameters in the tools are not there and the site is created without these tools(screenshot4).
This happens too in site info when trying to add tools. If select new tools, go to the next screen and press back and you continue again, then the tool options are not there and the tools are not added.