There are no such things as "stupid" questions. However if you think your question is a bit stupid, then this is the right place for you to post it. Please stick to easy to-the-point questions that you feel people can answer fast. For long and complicated questions prefer the other forums within the support section. Before you post please read this
How can I get Nautilus to ask for confirmation before deleting a file? Several times, it has failed to do this, although I think maybe sometimes it did ask. I looked in Preferences and "ask before emptying the trash or deleting files" is already checked.