I got Boundary Artifacts while using Cryptomatte.
I wrote a question on the same topic, and I read a comment that low resolutions could be an issue, and added a resolution perspective to write more specific questions here.
Rendering was done at 2560x1440 and layered the image using an Alpha Over node that takes the Matte output of the Cryptomatte node as a factor.
Even when working at high resolutions, the 1px Boundary Artifacts are still noticeable, and the more distant the object from the camera, the more vulnerable it appears.
How to use Cryptomatte correctly?
I've attached images and blend file to help you understand.
I watched the introduction to Cryptomatte from Blender Developer. And I saw connecting the Matte output of Cryptomatte to the factor of the Color FX Node instead of the Alpha Node.
I mocked this and created a new node tree.
However, Cryptomatte also seems to have limitations.
You tried to change the red petals to blue, but Cryptomatte doesn't mask the petals completely, so you can see the red color remaining on the border of the leaves.
(Please click on the image to see the edges of the blue petals at larger size.)
I tried a technique to adjust the mask area using the Dilate / Erode or Bilateral Blur and Colorramp nodes, but there were limitations.
After testing up to this point, I think there's an appropriate range for changing colors with Cryptomatte. If excessive color changes are required, re-rendering the 3D data seems to be the correct way to do it.