Why are some "gas" keys on 9 mm bolts angled like the FM9 bolts? I find it causes resistance when charging the gun because the angle pushes the charging handle into the top of the reciever.

Good question, and one of the reasons I went with Faxon.  It just doesn't seem logical to have an angle there.

That shouldn't be the case, the charging handle should engage the step at the front top of the bolt/carrier. The "key" on a 9mm bolt really only keeps the carrier/bolt from rotating in the receiver.

You are right. I broke out a 5.56 carrier to compare. The Foxtrot Mike carrier key angle starts right at the step. I measured it and it's only .05 inches high. Explains why I thought the charging handle was supposed to grab the angle by design. The step is shorter then a standard height step which is causing the charging handle to slip and grab the angle key.

Also relative to this is the cocking handles. Some are cut with a radius at the nose where it meets with the gas key, while others are cut angled at the nose where it meets the gas key.

On a standard AR DI system, that seems to have no effect, while the angle cut ones can jam a 9mm bolt up. Had it happen, could not for the life of me get the bolt to rack, it just locked up tight. Took me about a week on my first build to realize why it was happening.

I reached out to the company and they asked for a photo of my bolt. As soon as I sent it they responded that they are sending me a new bolt.
Here the two are. The bolt on the right is the defective bolt. The one on the left has more of a ledge for the charging handle to grab.