By choosing more than one node in a certain shape; while attempting to align with a component or a reference node in other shape, it results moving all the first shape to a new location (like I have chosen all its nodes)
Is there something wrong with nodes alignments … or I must have taken an overshot of Whisky 
Not sure I understand what you are doing. Can you describe steps, like 1, 2, 3, to reproduce the problem?
Here is a screen video explaining this:
Version 2.4 was working exactly the same. So that is not a new issue but rather a new feature request.