When I try to align various layers in GIMP 2.8, sometimes the align tool selects the entire image, not the layer I clicked on.
It doesn't matter how many times I try, and closing/reopening doesn't solve the problem. I've not yet discovered any regularities, it just seems to happen at random regardless of layer contents, size or position. It even happens with layers I'd previously aligned without issue.
Why does GIMP do this? Can it be fixed?
I personally find the align tool to be very little intuitive. I cannot reproduce your scenario, and the only thing I could imagine for the behavior you describe is if your target layer would have a lot of transparent detail, and would be hard to click on it (like in a layer with text with a small font). However, clicking repeatedly on the layer position could fix that - so I don't think that is your case.
Otherwise, what you are describing is just a bug in the program, that should be reported on the http://bugzilla.gnome.org tool, so that GIMP developers could know about it and fix in a comming release.
However, if you detail your use cases for the tool, I can try to come up with a script that would be useful for you right now, apart from the align tool. Such a script would require one to pick layers on the layer dialog, instead directly on the canvas, but it would work.
I had been having this problem FOREVER and I just found a solution, even though the person I was talking to about the move tool made me actually figure out the problem.
The alignment tool is selecting the top most layer where ever you click, regardless of what layer you have selected/transparencies. Try hiding the layers above what you are trying to work on, or move it to the top, use the tool, then move it back down.