I have noticed this occurrence in the past but I keep forgetting to post about it. It may be related to some other posts I have read regarding resume states with the plugin.
So, if I am watching a movie or tv show, there is a real time playback bar that will appear on the trakt website if I open it while playback is occurring. I have noticed that if I pause what I am watching or stop it in Emby, that real time playback bar will disappear on the Trakt website. When I go back and either restart playback or unpause, the bar on the Trakt website will basically reset and show playback as if the movie or show is starting from the beginning.
Once I am done watching whatever it is, it will still marked the item as watched on Trakt, but it seems like odd behavior for the real time reporting to Trakt to be off.
I tested this in that other server software out there just to check out this and the Trakt plugin over there acts normal when stopping or pausing a show/movie. In other words, if I stop playback and later restart playback, the real time bar on the Trakt website shows the correct playback from where I was before stopping/pausing instead of starting back at the beginning again.
So, this leads me to believe it has something to do with the Resume state reporting from Emby's plugin.