First, I just want to say that I am huge fan of the entire Halo franchise, and I've put hundreds of hours into the every game in the series. That being said, Halo Wars 2 is by far the MOST annoying of all of them so far about unlocking achievements. I'm playing on a digital copy of the game on my Xbox One. Let's start from the top:
When I first played through the campaign, I got all of the story achievements up to Hold The Line. Everything after that didn't unlock on my first playthrough. So, I decided to play through again to see if it was just a bug. I did, and the rest of the achievements unlocked just like they were supposed to, so I didn't give it much thought.
My next playthrough, I went after the bonus objectives, skulls, and campaign logs. Not too bad, except for the bonus objective where you have to kill 10 enemies with the light bridge. It was AWFUL. I got all of the achievements to unlock, except for the 100% completion achievements for the skulls and bonus objectives. The bonus objectives say that I have 82%, and the skulls say I have 60%, even though I have them all.
I am now playing through on Legendary, and even though I have completed several bonus objectives, the progress bar hasn't budged.
On to Skirmish/Multiplayer, I have noticed that, on several occasions, I will be playing, checking my achievement progress as I go, and suddenly I will stop accruing progess. On ANYTHING. the only solution I have found, which works occasionally, is to quit the game, sign out of my profile, then start the game back up. I still lose any progress I've made since then, but I will usually begin seeing a change in my progress after that.
To sum things up, this game is a lot of fun to play, but the lack of consistency on the achievements leaves you with a sour taste.