For example I put one diamond sword into the storage scanner (it is using chests, vanilla) but it shows that I have two diamond swords in but in reality there is only one, also it seems like the display number multiplies by 2 one stack cobblestone is displayed as 128 cobblestone. I use 1.19.2 and the ATM8 Modpack but I had this issue in other versions.

Show me some screenshots, your setup, the user interface

Show me some screenshots, your setup, the user interface

ATM8 Modpack Curseforge Latest version. For example I put 64 Cobblestone in there it is displayed as 128 but when I take it out it is still 64. screenshots:
https://github.com/McJtyMods/RFTools/assets/96308166/bf812655-e426-4e97-ab3c-332f00b79130

Oh, probably related to it being a double chest. I need to check how I can fix that

First, you posted this in the wrong github. This is for RFTools which is the old mod.
Secondly I can't really fix this. You just have to make sure not to include both sides of the same double chest in the scan