Strange things are happening.
I have items on the network and I can't remove them. After removing all the discs I can still see a lot of different items (no, they are not all in drawers), but I can't remove them. Then I made two energy input hatches, two were displayed, but I can only remove one.

Now it gets even weirder.
(I hope you understand.)

I then, with discs taken out lying in my inventory, quit the game a bit annoyed to write this issue here.

Then I thought I need a screenshot though and reloaded the game.

(My disks are still in my inventory!) I open the ME GUI and the non-removable items are gone. Now I put the disks back in the drive and they are back and removable.

But I am not sure if the quantities are correct! I was shown 10 signs, but I could only remove 5. The 5 are now completely gone.
I did build the two energy input hatches but the one I couldn't remove is also gone somehow. I'm not sure now if I had ordered two from the system.

To Reproduce
Sorry, no clue.

Additional context
pls, tell me what you need.

Environment

• Minecraft Version: 1.12.2
• AE2 Version: appliedenergistics2-rv6-stable-7.omni-fixes-v46n.jar
• Forge Version: 14.23.5.2855
• Modpack: Omnifactory STE

Just now I had that again. I wanted to take out some ores that were lying around in the system for a long time to create some space. I could take them out only partially. 10 instead of 20 for example. After a restart everything was normal again. Only 10 were displayed and I could take them out.
I use version v46aa.

So the way I fixed it: I removed all compacting storage drawers from my network. Storage controllers don't cause this issue

Removing all the drawers would be an impossible feat in my world.
The items that were not extractable (ghosts), however, were on normal AE2 storage cells.

I only removed compacting drawers. And also, in my world all items were duplicated, no matter if they were in storage drawers or not. I think that having compacting drawers causes computation errors in me system

I wish I could better English.

Strange thing is just happened.
I will try it to explain via screenshots:
I'm doing double packages to parallelize Draconic Evolution fusion crafting. Wyvern Core is my first item.
I have encoded and crafted the double package (I suppose you know what double packaging is).
And it is laying in the system:

The double package is encoded in a normal pattern, so I can order the Wyvern Cores:

Now I removed the fluix cable:

The ME-system is showing 2 packages now!:

I can remove one:

But I can't remove the second one:

When I place the fluix cable back, the ghost item disappears:

When I remove the one package and remove the cable afterwards, no ghost item is showing up.

The "bad" thing is, after I restarted the world (not the whole game) this bug is gone.

Greetings

Edit: STOP! It happened again! I posted this and a minute later it started doing the same thing.

Edit 2: Yes, I started the game a third time and it always happens. World download? :)

It even counts the liquids incorrectly:

After a restart of the world:

An important note.
This all seemed to have happened after I used the ME-IO port. Several times because I wanted to move items out to drawers.
Maybe the bug can be reproduced this way?

EDIT:
Ran all disks through the ME-IO port again, but unfortunately it didn't happen again.

I am having exactly the same issue.
for example, I have 10 fluix cables, I take all of em out and it leaves 1 ghost cable that still in the system.
And sometimes it duplicates all items in the system and makes half inaccessible!
Strange...

What version are you playing on? I haven't had this since version v46o.

I'm going to close this because it hasn't occurred since the changes were reverted.