MC 1.12.2
Forge-14.23.1.2587
ModularMachinery-1.12-1.8.1

I found this issue while playing the latest version of my modpack (https://minecraft.curseforge.com/projects/immersive-powered-factory), but the same issue appeared in playing another profile I newly created. Then I prepared some test json files of machine structure and recipe. Here are the links.

Machine : https://pastebin.com/BN4kbpYu
Recipe : https://pastebin.com/RfURQgh6

To reappear the issue, we have to prepare some liquid container to export liquid slowly, I just prepared Metal Barrel added by Immersive Engineering as it. Used version is the latest (Immersive Engineering 0.12 - 76)

1. Put 10,000mB Lava into Metal Barrel.
2. Configure upside of the Metal Barrel to export liquid with Engineer's Hammer, and connect between the output side and Fluid Input Hatch of the machine with Fluid Pipes.
3. Wait till all the processes finish, and open Item Output Hatch. Then you'll find there are more amount of cobblestones than 10.