When crafting a plate or fabricating something from a blueprint, I get the message that "1 (item) was burned". That item disappears and I am left at a loss when I was trying to profit from crafting/fabricating. When and why does this happen? I did not see anything written about this. If anyone could clue me into how not to lose money this way it would be appreciated.

You burn things when you fail at creating them. You fail at creating them because you wish your skill was higher. To get your skill higher, burn more items ... I mean, keep practicing. Your skill goes up a little every time you try.