These things are so annoying early on in the game as they seem to be everywhere but you can' do anything about them since you don't actually know what they are! Of course, if you're looking at this, it's a fairly good guess that you do now, so without further ado, here's the list of where all the magic chests are:
The asterisk (*) signifies that these chests exist in two separate eras (600AD and 1,000AD). The contents of these chests are all upgradeable, excepting the Guardia Forest chest. To get the upgraded items, open the chests in 600AD but DON'T remove the contents. Instead, return to where they are, but in 1000AD this time. They should upgrade into better versions and you can then swipe the 600AD ones as well for resale purposes.
Here's where the magic doors are; make sure to check them out since they've got some truly amazing stuff inside them: