I have been running into an issue with a specific combo of body/lens/filter that I cannot figure out. 90D, Canon 70-200 L IS F/2.8, any brand CPL. When I run this setup, the AF lands about 2-3ft behind the subject. The moment the CPL comes off, AF is perfect. I've used this CPL on other lenses on this body with no issues. These filters on that lens on other bodies works perfect. It's just this combo. Lack of light shouldn't be the issue as the f stop doesn't change the outcome and I am shooting outside in bright daylight. I ideally want to use the CPL as my next big event is all around cars, so reducing glares would be a massive benefit. Looking for any help at all.
I seem to recall that sometime back in the 2007 - 2008 period I had a problem with a Circular Polarising Filter and my Canon 5D MkII/Lens combo. I cannot remember the specific details now, but I resolved it by purchasing a better quality CPL. However unlikely it may seem, it may just be that your specific camera/lens/CPF combo are incompatible. Is there a chance you could borrow another or better quality CPF just to try it out on that camera lens combo?
Lets start with the CPL, its just a dark piece of glass. Which the glass itself can add a slight softness in general, more if its a lower quality filter. Focus should be able to focus through the glass, in fact the focus should be the same with and without the CPL. I use some very dark LEE filters i clip on with their system after composing the shot. Light Transmission will definitely be an issue, your CPL changes the exposure even if you keep the same F stop. in fact the camera when focusing isn't even using an f stop, it has not stopped down the lens at all (this happens only when the shutter fires). But it is working much harder to see through that sunglasses you put on the lens. SO its ability to read contrast on objects is inhibited, but inherently no it should not stop accurate focus. My assumption is its a cheaper filter not a B&W or the like if it is struggling, longer lenses will show imperfections in the glass of the filter quicker as at 200mm focus shift is in ft or yards instead on millimeters and inches.
I have tested with both K&F and Tiffen filters. I know these are not the top tier ones, but these work fine on other lenses, including a 24-105 L on the same body with no issue. It's not a softness issue, it's 100% a focus issue. After it auto-focuses, I can manually bring the focus a touch closer to me and the image is just as sharp as if there was no filter.
i did a googe search for clip in sensor filters, there re a few compatible with the 90d, might be worth a try?