I am not sure I understand, for example:
Lets suppose I have two clocks side by side that keep the same time for many years. One day I decide to move one of the clocks so it is now above the clock it was previously at the side of. Now, at the same time, by complete coincedence, the clock I move now starts to run slower than the other.
I could deduce from this that moving the clock caused time to slow down for the clock, but this would be fallacious reasoning as we know its just the clock running slower.
I am assuming the case is different for time dialation, that there must be reasoning and evidence that suggest time dialation as opposed to the atom vibrating at a slower/faster speed.