When aligning objects (say vertically), all object get aligned to the average vertical position.
This disturbs some other alignments.
Instead, the selection sequence should be given priority.
for ex.
For aligning rectangles A and B:
I select B first and then press ctrl + click (on A), then click align vertically
In this case it should keep B in its place and move A to align with B, instead of moving both to an average height.