Some experience orbs are grey when they are dropped (by bottles o' enchanting) and summoned (by command block).
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What I expected to happen:
Every XP-orb has the same yellow-green color
What I saw:
Some (around 5%) XP-orbs are grey.
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Steps to reproduce:
1. Give yourself a command block (works faster, bottles o' enchanting work too, but it is slower)
2. Put in the command block '/summon XPOrb <number of choice>'
3. Put the command block on 'Repeat' and 'Always Active'
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If everything goes right, then you can see some grey XP Orbs between the normal ones. If not then I'm probably the only one =P
EDIT: Is probably a dupe of MC-92915
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Duplication of MC-92915. Make sure to vote that up.

@Michael Wobst Did it, I thought it was only the XP Orbs that are affected
This is Intentional I believe. What is happening is when you pick up the exp it goes transparent. If you pick up an item it does the same. I believe it is for people who can have seizures by repeated drastic changes in light. Which is why they made it so you pick up the exp at your feet.