when working with stain and wood i always sand away the stamps before staining, i dont know if that is how normal people do it :D good luck!
The prep for the staining was not done correctly. If there is any stamps on the deck surface, they need to be cleaned off and the board(s) sanded to allow the stain to be accepted to the surface in an equal way. You may be able to sand those areas and re-stain them so they blend into the new finished surface. But do not wait to long as the stain will fade and the new stain will not match for some time after it is applied.
Part of the problem lies in your lumber choice and how it was installed. Higher end decking is not stamped ( like tropical hardwoods) softwood lumber may or may not be stamped. When the lumber is installed the installer should have set the boards with the stamps facing down not up...I have yet to see lumber stamped on both sides.
If the stamp side was exposed then it should have been prepped better...by sanding. I have found that 80 grit keeps the wood rough enough to prevent glossy areas when semi- or transparent stains are used.
To fix this you will need to sand as Woodbridge mentioned above, ideally the sooner the better. To minimize the sanded look you will want the "feather" out the sanding edges.