I have not seen this reported before. You found the charm before your last saved?
The only issue with charms I recall is that they must be in your inventory to use, not in the battle tower chest (which obviously isn't the problem in this case).
If you select the helmet and try to charm it, do any charms show up in the list?
After adding a charm to equipment, it shows up in the item description (the 'empty charm slot' icon and description are replaced with those of the charm).
