Is this what you are referring to? https://i.imgur.com/AN6bc8S.jpeg
I just checked, and it seems to be an issue even without the HD graphics mod. My assumption is that this is a new ground decoration in the base-game that is not getting removed by the new tiles.
I'll try to look into solutions (I probably just need to increase the asphalt's tile layer), but I can offer a work-around for now: There is a mod called Lawn Mower that adds a button that can be used to clear decorations in an area. That will at least allow you to clear these patches manually.
If this is something different, please link me to the specific HD graphics mod, and a screenshot.