Later in the game when you get to the time period Antiquity you get Marle's Pendent powered up and then you can open up those chests.
Also note some of those chests are in the location but in a different time period look in the chest but don't take the item out of it why if you do so the item that was in that chest is powered up in the future.
For example if you find a chest in Middle Ages and go to the same location in Present and chest is there look inside in Middle Ages chest but go to Present and you'll get a upgraded version of what was in that chest if you had actually taken the item out in Middle Ages also because you took out the item in Present the lower grade version of that item is still in the Middle Ages chest.
Holy cow! I haven't talked to you in so long!
I'm glad to hear you are good. I'm alright. I'm really tired. School is hard, but it is going alright. ^^
It is great to hear form you.