Describe the bug
As above. I can view them in the ME system, but not take them out of the system, and JEI says they're missing if i try to paste a recipe into the crafting terminal. This behavior goes away after exiting and re-entering the world (without reloading Minecraft itself), or removing then replacing the ME storage cell with the problematic items in it.

Additional Note: Even the first time I view the items' uses in JEI, it always says they're missing from the system.

To Reproduce
While using a Crafting Terminal (This only happens with a crafting terminal, a Pattern Terminal acts as a work-around), press the "Uses" hotkey in JEI on an item in the terminal, in your inventory, or in the JEI window. (The bug does not happen if you check the uses of an item without the terminal open)

This only breaks vanilla items with vanilla recipes. All modded items I have tested work as expected, and vanilla items without vanilla recipes but with modded recipes work as expected. In my case, for example, checking the uses of pumpkin seeds doesn't cause any issues, even though they're used in modded recipes, but checking the uses of a pumpkin puts the stack of pumpkins in the weird state described above.

This minimal setup recreates the bug:

But only when using the Crafting Terminal.
(The block on the bottom left is just a creative energy source from Draconic Evolution)

Expected behavior
The expected behavior here is for nothing to happen.

Additional context


(How iron ingots look in this state, in both JEI and the ME system)

Environment
Singleplayer

Modlist: (o n o)
Just Enough Items - 4.16.1.301
Mantle - 1.3.3.55
Chisel - MC1.12.2-1.0.2.45
CTM - MC1.12.2-1.0.2.31
CodeChicken Lib - 3.2.3.358
Shadowfacts' Forgelin - 1.8.3
CoFH Core 4.6.6.1
Immersive Engineering - 0.12-89
Biomes O' Plenty - 7.0.1
Tinkers' Construct - 1.12.2-2.13.0.183
Industrial Foregoing - 1.12.13
Thermal Foundation - 2.6.7.1
Mekanism - 1.12.2-9.8.3.390
Redstone Flux - 2.1.1.1
Fast Leaf Decay v14
Thermal Expansion - 5.5.7.1
Mekanism: Generators - 1.12.2-9.8.3.390
Thermal Dynamics - 2.5.6.1
TorchMaster - 1.8.4.84
Thermal Innovation - 0.3.6.1
CosmeticArmorReworked - 1.12.2-v5a
Blockcraftery - 1.2.0
Engineer's Decor - 1.1.1
ProjectRed Core - 4.9.4.120
ProjectRed Exploration - 4.9.4.120
ProjectRed Fabrication - 4.9.4.120
ProjectRed Compatibility - 4.9.4.120
ProjectRed Illumination - 4.9.4.120
ProjectRed Expansion - 4.9.4.120
ProjectRed Transmission - 4.9.4.120
Dynamic Dynamos - 1.12.2-1.10
Ender IO - 5.2.66
Mystical Lib - 1.12.2-1.9.0
Tesla Core Lib - 12.2-1.0.17
EnderCore - 1.12.2-0.5.76
MrTJPCore - 2.1.4.43
Forge Multipart CBE - 2.6.2.83
CoFH World - 1.4.0.1
Techguns - 1.12.2-2.0.2.0
Drawbridge - 1.2.1.8
U Team Core - 2.2.5.147
PeacefulSurface - 1.12.2-v2
Ender Crop - 1.12.2-1.6.0
CustomNPCs - 1.12
Dimensional Doors 3.0.9
Craftable Glowstone - 1.0
Railcraft - 12.0.0
MoarSigns - 6.0.0.11
Wings, Horns, and Hooves, the Ultimate Unicorn Mod! - 1.5.16
Just Enough Resources - 0.9.2
Ore Veins - 2.0.15
Better Bedrock - 5.1.11
Waila - 1.8.26
T-Square Builder Tools - 1.0.7
Draconic Additions - 1.12.2-1.17.0.45
Draconic Evolution - 1.12.2-2.3.28.193
Advanced Rocketry - 1.12.2-2.0.0-13
libVulpes - 1.12.2-0.4.2-25
Baubles - 1.12-1.5.2
Brandon's Core - 1.12.2-2.5.19.214
Energy Converters - 1.3.7.30
HBM's Nuclear Tech - Extended Edition - 1.12.2-1.9.5-I
Iron Chest - 1.12.2-7.0.67.844
JourneyMap - 1.12.2-5.7.1
AE2 Stuff - 0.7.0.4 (this mod's been behaving oddly as well; the Advanced Inscriber doesn't accept certain items, idk if that's a known issue or not)
AE2 Unofficial Extended Life - rv6-stable-7-extended_life-v0.55.13
BD Lib - 1.14.3.12
Fullscreen Windowed - 1.6.0
Inventory Tweaks - 1.64+dev.151.822d839
Mouse Tweaks - NONE(?)
Better Builder's Wands - 0.13.2
Integration Foregoing - 1.12.2-1.11
GunpowderLib - 1.12.2-1.1

• Minecraft Version: 1.12.2
• AE2 Version: The name of my jar is "appliedenergistics2-rv6-stable-7-extended_life-v0.55.13". I'm not quite sure how you're notating versions, it's just the latest ver that Prism launcher downloaded through CurseForge.
• Forge Version: 14.23.5.2859

I poked around a little more and realized I overlooked this issue!
https://github.com/PrototypeTrousers/Applied-Energistics-2/issues/261#issue-1657801631

Removing CustomNPCs fixed my problem. I have not the faintest clue why that would affect anything, but the crafting terminal is now working as expected! ^w^