I've had this issue on both my Titan and Hunter today while using an arc subclass. Seems like elemental wells and orbs are not providing stacks of charged with light despite having both the "Elemental Charge" and "Taking Charge" mods equipped on my armor. Not sure if this is unique to arc subclasses or all encompassing but curious to know if anyone has experienced the same thing.
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To make use of any mods that use a charged with light, you will need to quip the actual mod that lets you become charged with light while picking up orbs or wells, make sure you have that one equipped