In my experience with newspaper ads they should be supplied the exact dimensions of the ad hole. Page collation/layout software like Atex CyberPage and Pongrass have specific size place holders for booked ads when the ad file (be it PDF, EPS or other) has passed QA it will match its booking number and pop into its ad hole.

NO crop marks, registration or color break downs should be attached as the prepress department just has to remove all the clutter and then crop the PDF image to the right size using Pitstop Pro and Acrobat before putting in to the system. That's if the newspaper even has a production department anymore. Which would make sense in them asking you to resupply the ads at the correct dimensions.

More on printers marks:

Crop marks are need for die cut and guillotine work, so are pointless being on the ad file they will also scale the ad down and stuff up the ad in size if not checked before being placed.

Registration marks will be added to the final page PDFs for the printers to line up the plates when printing so have no use on the ad file.

Newspapers use CMYK and nothing else so there is no need for color bars with spot colors and the like.

If the ad is full, half page or a custom ad and the press can print edge to edge then bleed can be used.

Bonus tips:

Newspaper presses generally have a print resolution of 150lpi which works out about 200dpi. So image quality never needs to be any more than 300ppi.

If the ad has a border make the stroke is set to the inside of the frame.

Avoid multi plate blacks with extra color percentages. As this can mess with the registration. Use 99% black as this can avoid over print issues on older CTP machines.

And always export or convert to CMYK being sure to remove spot color.

When you were told to add a margin/gutter to your ads was a reason given?