I'm certainly never manually attaching anything. Usually they're made by printing to .ps and distilling. (That's how our prepress department requires the files be made, and I prefer to do it that way in most cases since it minimizes preflight errors.) If there are flattening issues I export directly from the original application to PDF. I don't know of a step that would automatically turn anything into an attachment. I can check the Attachments Pane next time and see what attachments it thinks are there. That might help me figure out where they're coming from.
It doesn't seem to create any problems to let Acrobat strip them from the file. I've just been wondering what this means.
