Since the release of Witch Queen, instead of using Taking Charge, I've swapped to using Elemental Charge due to the higher and more reliable drop rate of wells vs orbs of power. Ever since I did that, I've noticed that when there are two elemental wells on the ground next to or close to each other, it will only give me 1x Charged with Light instead of 2x when I run over them (or 2x instead of 4x if they match my subclass). This never occurred with Orbs of Power, so I'm thinking this might be a game registration issue when the player runs over two wells in quick succession. It's like there's a cooldown with the game registering the player picking them up, so it gives you the Charged with Light stacks for a single well instead of both that were there.
In the video I attached to this post, I am using both the Charged Up and Supercharged mods (max of 5 stacks), yet you can clearly see I go from zero stacks of Charged with Light to only 2x Charged with Light, despite the fact I ran over 2 wells that matched my subclass energy and should have gotten 4x Charged with Light. It did not register that second well for my Light stacks, yet my grenade cooldown registered the two wells and gave two distinct bursts of cooldown reduction in response. When I picked up that solo well by itself 5 seconds later, it gave me the 2 additional charges, yet I didn't get 4x stacks when I ran over the two wells next to each other like I should have gotten.
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Some mods that give elemental wells additional functionality have a small cooldown to them. For example, if you pick up an arc well while having Well of Striking equipped you'll get the base amount of energy plus the additional melee energy. If you immediately pick up another arc well, that one will only give you the base amount of energy. I'm guessing elemental charge also has that cooldown.