Everything is traveling in time —so far, in one direction only. The examples you give can all be explained within the bounds of today's known science and tech. To pick an easy one; some old coke machines will likely become collectors items & some of them will be lovingly restored.
Meanwhile, it remains impossible to move backwards in time. When objects from a (relative) future appear in a scene set in the present, that's clearly a mistake. One we call an anachronism. Those are the sorts of anachronism we rightly criticize.
I completely agree with your last point. TOS operated on a shoestring budget for effects and props.
Thanks to YouTube, I have found the scene in question.
https://www.youtube.com/watch?v=-sCPnrRJFT4
Looking at it more closely, the wrench definitely changes from the one he grabbed at 3:53, into something larger, and looking more like a fixed crescent wrench than an adjustable wrench. Maybe the wrench is actually presenting itself as something different than what it really is, like the “Western Electric” old phone ring setting I have on my iPhone. Then, it changes shape after being grabbed to its real self. That would explain the whole thing!