Krita supports per layer colour space. As in each layer can be in a different colour space and profile like CMYK, RGB or grayscale. Photoshop doesn’t support this. So krita is warning you about it.
Either find the layer which has different profile and convert it’s colour space to the one you are using for entire document or apply the colour profile for entire image again.
If you want to check which layer has which colour profile then you can inspect layer properties by F3 key. Find the layer and then convert only the layer colour space via layer menu > convert > convert layer color space. This is tedious job if there are lots of layers. And
The quick way is to go to the image menu > convert image colour space.