Using a portal gun on the compact machine walls causes the portal to dupe and bug out.

What does "causes the portal to dupe" mean?
What kind of walls are you talking about? The solid ones or the craftable ones?

It is the compact machine walls inside the compact machine. I am honestly not 100% sure which mod is at fault, but I can say with certainty that when a portal was on the machine walls (the unbreakable walls), it bugged out like no other, but if I put some dirt and then the portal on the dirt, it was fine.

This seems to have nothing to do with Compact Machines.
Using the Portal Gun in the Nether has the same effect.

Please open an issue in the Portal Gun issue tracker.