Face nails gets filled with color/specia matching wood putty, cheapest installation option, which is standard. For a Additional charge, if, your contractor offers it, the option of a face nailless installation to avoid this swiss cheese look. It takes more time, additional fasteners and work is needed, you have to allow extra time for flooring adhesive to dry before moving ahead to sand and finish. You get what you paid for.

Sounds like you weren't expecting this. Look over your paperwork and any sample board you relied on for your choice. I wouldn't accept this type of installation. Or pay for it.