Version: 1.21.1
Modpack: ATM Arcana

I have Quantum Bubble equipped and it appears to lift up my create contraption (just a basic create tree farm) and then I have to dismantle and reassemble it to fix. Is there a way to blacklist create contraptions from the effect or something?

I just had something like this happen to me with the item.

With the Ars Nouveau Scribe's Table, any item being taken from storage or output, the traveling required item with be taken by a bubble before it eventually pops.
The table still crafts with it, but the fact it still happens means it is being used like a projectile, similar to the machine of yours there.