Here is one of the crafts :
https://puu.sh/E6I0O/5b02c5c853.png

Here is what it shows in the molecular assembler :
https://puu.sh/E6HZN/47e806353f.png

The pattern was made correctly :
https://puu.sh/E6I23/ef7b4f89ad.png

Here is another craft that doesn't work in Thermal Foundation

https://puu.sh/E6LfS/434a18a9f2.png

I spot plugin related mods, is this an single player issue? Can you confirm this happens in single player?

Please report all autocrafting related bugs directly to your modpack as most are using addons which intentionally break it.

This is a custom modpack I made, nothing was meant to break it

Then the infortmation requested in the template might be useful ...
AE2 version
Forge version
Minecraft version

Additionally a list of the other mods and their version would be very helpful.

Minecraft: 1.12.2
Forge: 14.23.5.2838
AE2 : rv6-stable-7

Other mods :
CodeChickenLib-1.12.2-3.2.3.357
CoFHCore-1.12.2-4.6.3.27
CoFHWorld-1.12.2-1.3.1.7
MRCrayFish's Furniture-6.3.0-1.12.2
Just Enough Items 1.12.2-4.15.0.287
MovingQuickly-1.12.2_1.0.0
RedstoneFlux-1.12-2.1.0.6
ThermalDynamics-1.12.2-2.5.5.21
ThermalExpansion-1.12.2-5.5.4.43
ThermalFoundation-1.12.2-2.6.3.27
Thermal-Solars-Mod-1.12.2
Voice Chat Reloaded-1.2.0
WorldEdit Forge-mc1.12.2-6.1.10

Hey, so in fact i'm a total noob and i used 6 interfaces on the molecular assembler. Output wasn't connected to the network. Everything is working ...

And this was on a forge server, but it's not relevant anymore then

So the issue was, that the m. assembler wasn't powered. You can only attach 5 interfaces on to 1 ma., because at least one side needs to be connected to power (usually a normal me cable without interface)