I replayed Half-Life 2: Episode 2 earlier this year, getting all the remaining achievements that I didn't get in my first playthrough. 

So to my surprise, when I was just looking through my Steam list I noticed that I only had 95% (21/22) of the achievements - it tells me I'm missing Neighbourhood Watch. I know that I definitely got all of the achievements in the game, including Neighbourhood Watch. 
 
So I decided to fire up Episode 2 and double check. Sure enough, in game it tells me I have 100% of the achievements, but on Steam it tells me I have 95%:
 

I'd never heard of this before but after a bit of Goggling I've discovered that there are quite a number of people who have run into this issue. It's by no means a recent thing, in fact this issue seems to have been around for quite a long time but unfortunately people seem to be saying that there isn't actually a fix for this and it's something Valve have to sort out on their end. I hope Valve do get this sorted out at some point because it seems to be a pretty major problem and it must be a bummer to run into it.