Do you trust batting numbers when they fluctuate year-to-year?
Batting numbers are what they are, they are pure results of at bats. Defensive stats are people reviewing and assigning value.
I also like to look and see the reasons with fluctuating stats. There's a difference between stats just fluctuating and being affected by playing time, injuries, or whatever.
To me, if there was a camera say on top of the upper deck facing down on the field, and you could digitally map zones based on the starting point and ending point of a player's movement (I know it's hard to explain in writing over the internet) I would feel slightly better, but then someone still has to judge the difficulty of the play in particular. No two fly balls are the same, no two line drives are the same, then weather, field conditions, and SO many other variables enter into things. For loose reporting and following, I don't see anything wrong with how things are right now as long as you treat them closer to a play official scored, than as a factual hard number. Also don't think they should be included in WAR calculations. They are better as a non-component that you can look at in conjunction with WAR instead of included in it. I mean, how much more terrible does someone have to be from one year to the next to have -21 more dWAR, and how were they THAT good to accumulate 24+ dWAR in the first place? There are just too many little instances like this where you ask for what accounts for that and no one is entirely sure.
I think someone over at fangraphs said it best on Twitter a little while back (paraphrasing) that they weren't perfect, but they were the best of what we had at the moment, so take them knowing that.