I'm not quite sure how to prove this through a log or a video if I manage to catch it, but since the version 0.4.1 Enigmatica 6 debuted, I occasionally lose items when requested them. All I can tell after testing is that it might be related to when you ask for 64 of something that doesn't have that much. Still testing as I go to see if it happens using exact numbers... If there's anything else I can gather let me know. Hopefully this is the right spot!
My most recent example:
Had 44 wheat in a vanilla chest hooked up to pipes, only a low speed extractor on a pipe attached, along with a pipe pressurizer.
Requested 64 with the shift click, I got exactly half the stack instead, and the other 22 disappeared.

I tried to leave the server and reconnect afterwards to see if it was client-side, it doesn't appear to help.

Yup, I see what happened in my setup. I'm sorry for taking up your time. Thanks for working through it with me.

If you can't consistently reproduce this issue, it'll be hard for me to attempt to fix it. I think your best bet would be to try to recreate a simpler version of your current setup in a creative world and narrow down what exactly might be causing the issue. Any slight anomalies you find would help, really!

Well, about 30 minutes in creative and I'm really unable to replicate it. Maybe something going on with the server? I'll keep at it and let you know.

Alright, definitely seems like it's something server side, or maybe setup wise. I just had two happen in a row, one was using 64 to request a smaller set, and the other was an exact retrieval amount, both halved the items on retrieval. I'll see if I can clone the server world and test locally.

Update - I've been checking the chest contents back and forth, and I actually think it's reporting double of what is in the chests. Still not able to replicate it locally, however. But the doubling makes it look like I'm losing items, and also explains why it's always half back.

Do you have your chests connected to the network twice? That would explain the double item reports.