Experience Orbs have been getting stuck for years, where they cant be collected, burned, or voided. Well, I may have solved the mystery. The orbs are simply misplaced. 
I tried tping orbs to a different location.

What I expected:

The orbs would tp

What happened:

They teleported but looked like they were in the same spot. They could be picked up if you went to their real location. Relogging fixes it.

Steps to Reproduce:

1. Put 2 repeat command blocks with levers and Needs redstone
2. Put ‘summon xp_orb ~ ~1 ~’ in one, and ‘tp @e[type=xp_orb] ~ ~ (number)’ (with a tick delay of 5) in the other.  Put a box around that location.
3. Flick the summon xp one
4. Flick the teleport one
5. Unflick the summon on
6. Try to pick up the orbs. Then, go to the location you tried to teleport them to. Some will show there but most won’t. You can collect them ALL from there though.

Thanks for reading