Troubleshooting immediate CAFI Trip
It's possible you have a ground wire nicking a hot or neutral. The easiest way to remove that issue is wrap the outlets and switches with a couple loops of electrical tape so the screws are covered.  I do that in metal boxes/EMT, and that doesn't even have ground wires.  Also, if the screws are all the way out because they came that way from the factory and you use the backstabs, that creates a larger surface area for that to happen, and the answer is stop using backstabs!  

However the more likely threat is your wiring topology. 

The most basic rule is currents must be equal in each cable.   Now, the rule is relevant to EMF emission (on a balanced cable, all currents cancel each other out, so their EMFs do also).   However, it's also relevant to GFCI, AFCI and CAFI, since those are looking for differential current as a sign of a ground or arc fault.  But this rule has a very valuable corollary: 

Tree topology is safe. Mesh topology is dangerous.

If you consider a tree, it has many branches, but the branches never rejoin. Quite different from a roadway system, which is a mesh - you aren't obliged to go back the way you came.   Consider ants exploring a tree all day and going home in the evening. Ants can't jump branches.  You could put an ant turnstile anywhere on the tree, and if 130 ants went up past that point, 130 ants come back down.  Currents are equal anywhere in the tree.  

So as long as your wiring topology is that of a tree, it's hard make a shared neutral mistake. 

Now, sometimes your cable topology needs to enter a box from 2 separate directions (e.g. that 3-way case). You can either use 2 boxes, or you can use a box divider (real or mental) to fully separate the cables so it's effectively 2 boxes.  

Nowadays with GFCI you have to be really fastidious about this stuff. Before, you could play fast and loose and it would "work" if nobody put a clamp meter around the cable, but that GFCI or CAFI is the clamp meter. 

Multi-wire branch circuits need a 2-pole GFCI/CAFI

Perhaps you are using an older trick: the Multi-Wire Branch Circuit or MWBC, also called a "shared neutral" circuit.   Two hots on opposite poles share a neutral. Perfectly safe and proper when done correctly, but doesn't play well with single pole GFCI/CAFI. You need to use 2-pole GFCI or CAFI for that.