Assuming that the Xbox Achievements are the same as the PS4 Trophies I should be able to tell you what you are missing if I know what you have already because I've obtined all of the PS4 Trophies for Garden Warfare 2.
Many of the Secret ones are related to the single player Quests, and if memory serves two of the newer ones concern unlocking the Backyard Portal to the Trials of Gnomus and one is for completing the Trials and freeing the Torchwood and Hover Goat 3000 from Gnomish imprisonment. Both of those have only a low percentage of Players earning them.
Another set of Secret Achievements with really low completion rates has to do with Infinity Time and defeating the King of Summer, King of Winter, King of Spring, King of Autumn and King Gnomus himself.
If you earned all of those already then I can check to see what other PS4 Trophies have really low completion rates since it's probably mirrored in the Xbox completion percentages as well.
looking at achievements it's kinda sad how is something as common as completing a quest only 33% of the 1 million people playing have done 1 quest?
