Are the sprites significantly downscaled? What do the exported spritesheets look like?
Currently WebGL mode can create mipmaps for high-quality downscaling, but only when the source image is a power-of-two size. Spritesheeting means every image on the spritesheet can use high-quality downscaling, but some leftover images can end up not on a spritesheet, end up with a non-power-of-two size, and then have to use low-quality downscaling. So the ones which you think are blurry are actually using a higher quality downscaling, whereas the crisp ones are actually aliasing due to undersampling, which looks higher contrast, which can be mistaken for higher detail.
You could try setting downscaling quality to "high", which uses more memory but should at least be consistent.