Hi, this question may sounds noob but I’m new making mods.

When I place an objet (like a crate in a world cell, only this thing, without touch anything else), and then I delete the crate, the cell appears marked with ‘*’ forever.

Then I use ‘File -> Data -> Details’ and I delete this reference, but It remain a mark ‘– D’ and its never gone.

Can I delete a reference in ALL ways? (Like I never touched it before).

Use TES4Edit to easily remove dirty edits.

Short answer: above.

Long answers:
http://cs.elderscrolls.com/index.php/TES4Edit/Mod_cleaning_tutorial_with_TES4Edit
and
http://cs.elderscrolls.com/index.php/TES4Edit_Cleaning_Guide

No matter what changes you make, they are considered a change. Something like deleting an item you accidentally created or setting the coordinates of the object you accidentally moved back to what they were will be still considered a change. It is recommended you make a backup to all your mods, to avoid these unpleasant things. Solution was already given above:)

Adding and then deleting an item probably won't show in the saved plug-in, but a more likely situation is an unintended move or delete of something that's in the base esm's. You should run a TES4Edit clean-up anyway, just to check that everything was intentional.

I ve just done the tutorial of the TES4 Edit, thanks!

If it's marked with a -D and then you save it, just close the CS and then reopen the CS with the mod and the reference should be gone.