I know what you mean I've noticed since after the first few races, Hamiltons pit stops usually end up being better 5 tenths and 1.5 seconds slower, a few times it has cost him track position if not to Rosberg then someone else.. I don't buy into any conspiracy theories either, just find it strange as to why it happens so much.
Could be many factors for this whether it is pure luck or maybe Rosberg aligns himself better in the pit lane, stops to a halt and goes off 0.1 quicker than Hamilton, maybe Rosberg practices his pit stop way more than Hamilton and has it more refined etc. I am always dubious of any conspiracy theories!
You quite often get this with most teams where one is consistently getting quicker pitstops than their teammate repeatedly. To me, it is more a sign that one driver and his mechanics have worked harder at the pit stop routine and are therefore doing it more on instinct in the race without needing to think about it so much.