The issue with them not working in alternate realities could be one of frequency alignment. Obviously there must be some sort of quantum vibrational difference that separates realities otherwise everything would all just be a soup of quantum energy with no sense to be made of any of it. The more different two realities are to one another, the more misaligned they became.
Think of alignment as a 360° rotation with the "original" timeline being 0°. Every year of separation in events branching timelines will rotate 0.1°. A reality which seperated from your own 10 years ago would only 1° apart, whereas a reality which separated 1800 years ago would be °180 apart, completely opposed to the control reality. Instead of a closed circle, this rotation would be on a spiral, thus preventing realities from "reconverging." 1800 years of separation would yield VERY different realities, with entirely new societal paradigms, and it's unlikely any of the same people would even exist.
Think of the stones as being "calibrated" for their own realities vibrational frequency, they might work if the realities are close, but less so the more apart they are. For the sake of argument let's say my above example was correct math. Two of the stones came from 1970, and four of them came from 2014, but since the stones work in tandem, their offset would be averaged at a 2.56° rotation. If we think of 180° as the point of no return where the stones become 100% ineffective, a 2.56° rotation would yeild a 1.42% margin for error whenever the alternate reality stones were used. 1.42% would be 142 out of every 10,000 actions, and every person or thing brought back would be a separate action.
Now of course my math probably isn't exactly right, the margin for error could be far less or far greater than my example, but considering how many people there are the universe, even a 0.0142% margin for error could have devistating ramification when you consider what errors could mean. A margin for error doesn't necessarily mean failure, only error. Maybe one of those errors is that the same person is brought back twice, or someone who didn't have superpowers now does have superpowers, or someone who did have superpowers now doesn't. Someone could be brought back younger, or older than they should have been. And of course straight up not bringing someone back is also a possibility.