Note: typing this on my phone, sorry for any misspellings
So I had this same issue, but it was mainly cuz I didn't know how focus worked. "Focus" skills are button combos, with your focus bind being the first part, and then something like companion attack or later abilities will be the second, so companion would be by default R1+Square, so when u rebind focus to say L2, the result is L2+Square.
Additionally, I also spent some time getting my controller mapped similarly to dark souls, and I've gotten everything to work (except for a few bugs, yes actual bugs, I'll talk about them in a second) here's what I did
Attack-R1
Parry/block-L1
Jump-X
Evade-O
Special attack-R2
Heal-Up
Ascension cable-Square
Interact/target-R3
Map-touchpad
Sprint-L3
Stance1/2- left/right
FOCUS-L3
companion assist-square
Push-triangle
Pull-square
BD-1 fire-square
Everything else was left to default, I am about 10 hoursish into the game and I've had no problems when it's not bugged (I've included some default in the list above just for clarity)
Now for the bugged parts (minor early game mechanical spoilers)
With these controls, you must restart your game for the ingame prompts (ei grapple) to show up with the right keybind.
If u rebind focus, when u attempt to tame a creature for the first time, it will display the correct button that u set it to, but it will not work. Hitting the original key bind (R1) will do nothing. You can fix this by rebinding focus to R1, hitting the prompt, then u can set it back. Very annoying hopefully it's patched soon
The most annoying bug of them all, and if I could get some signal boosting on this that would be great, is that if u rebind ur special, while u have blaster stance on, your blaster will still be bound to triangle, even if there's something else mapped, and R2 will do nothing. This is only an issue for the blaster stance, all other specials work just fine. There is no way to fix this right now, and what will happen is upon hitting triangle, it will either do ur bind or shoot and it's very inconsistent. This has made it so blaster is practically unplayable for me unless I use the default controls which is very unfortunate because that was the stance I was most excited about.
Hopefully this helped you out, i know those bugs are very inconvenient but I'm hoping theyll get patched soon. If someone does find a fix for the blaster stance PLEASE let me know