After talking to PeachizXD more, it seems like summoning the pharaoh, then leaving Atum and coming back, then killing the pharaoh causes the issue.

They had died before getting the pharaoh kill. Not sure if they /home back or used some other way.

You can see this issue for more information. Let me know if you have any more questions.

Thank you for the report!
I've been trying to reproduce this quite a bit. Tried teleporting around, using /home (FTB Utilities), switching dimension, dying etc., but it have worked just fine for me every time.
I would need you to provide a consistent way to reproduce the issue, or a world (With as few mods as possible), with you standing in front of the sarcophagus that cannot be opened :)

An additional note of info: a creative mode player can break it and have the items drop.

See: SmashingMods/antimatter-chemistry#57 (comment)

happened to me just now, can confirm. playing antimater chemistry modpack

Please provide a world where it's happening with coordinates to the pyramid.

I have the same issue. It always occurs once the chunk of the pharaoh and his sarcophagus is unloaded.
So to reproduce:

1. You summon a pharaoh
2. Exit the world to the main menu (chunks get unloaded)
3. Rejoin the world
4. Kill the pharaoh
5. Sarcophagus is bugged and can't be opened

Edit: The problem is that when the pharaoh is created from NBT it uses the EntityPharaoh(World world) constructor. There it sets the hasSarcophagus to false. Hence it can't unlock the sarcophagus on death.

Thanks for giving some more insight!
If you could provide a world where it happens that would be great, because I can't reproduce it with those steps.

So i installed Atum 2 and Optifine.
Then i created a normal world with the seed: 3916825317961709452
Then i built a portal and searched for the nearest Pyramid. Sacrophagus room at 90 57 320
I placed the Royal Torches and right clicked the sacrophagus.
I clicked "Save and Quit to Title".
I rejoined the world and killed the Pharaoh.

That is the world with 3 torches placed at the sacrophag.
TestWorld.zip

Thanks a lot for the test world @Meldexun, I would not have been able to fix the issue without it - as I can still not recreate the issue following the exact same steps in a new world.
The fix will unfortunately not fix the issue for Sarcophagi that have already been affected, but it'll fix new ones.