When encoding patterns using the Pattern Encoder it will miss some components required from crafting.
I think it happens when you have the pattern for the component available (can be crafted) but you don't have any of said component in your ME Network.

As you can see in this screenshot it's missing the Machine Frame from TE, which I encoded earlier but did not craft. I then crafted a Machine Frame and tried to encode the pattern again and the Machine Frame was there.

i have noticed this as well.. imho its a bug.. the pattern encoder imho is meant to encode patterns/be better then the normal screen.
i don't see a point in using it when it can't just make the pattern. I recall it use to in 1.7.10 so i am guessing it was removed?