Disclaimer: I may not know what I'm talking about, feel free to correct me if you think I'm making a fundamental error.  I just got a bread machine and I love it.  It's so easy!  But I'm experimenting.  The first time we used it, we used a store brand white all-purpose flour, and the bread simply wasn't very good.  It was crumbly, it collapsed a little in the bread machine, etc.  I mean, it wasn't bad, we ate it.  But I wanted better.  After that, we bought King Arther white bread flour, and it worked much much better.  The bread was delicious with a wonderful texture.  I don't know how much of this is because it's bread flour (I assume mostly this) and how much is because it's a nicer brand (I assume this is a smaller factor).  It's great bread!  However, I'm told that white bread in general is not as healthy as whole wheat bread, although I'm not exactly sure what whole wheat means or how much healthier it really is.  Therefore I want to make "whole wheat bread," whatever that means, in the interest of health.  And to be honest, I've had some very boring whole wheat bread, and some incredibly delicious whole wheat bread.  It varies.  So, what do I need to do?  I assume it's a question of getting the right flour, but I didn't see "whole wheat bread flour" in my store- is this because it doesn't exist, or because my store doesn't carry it?  What should I be looking for?  Any tips, specific or vague, would be appreciated.  Thanks mmuch. 
This occurs pretty often with leeks as well.  The procedure there is to cut open the stalks lengthwise - i.e. one cut from top to bottom along the long axis.  This allows you to fan apart the layers to ease out any trapped dirt.  You could do the same thing with your green onions, assuming you don't mind cutting them lengthwise.  If you don't want to cut, you could try soaking them in a sink or pot full of clean water for a half hour or so, agitating them every now and again.  The water should get down the stalk and at least loosen up any trapped dirt. 