EDIT: Fixed it… there was a 1x1x1 unit gap.
In your log it usually says the name of the entity getting leaked. Look at your compile logs again. Or better yet, post them here.
Try to turn off brush entities and point entities and etc except for world brushes in the visgroups if you haven’t done so already to narrow it down and recompile and etc. I don’t know about the red line not touching anything, but maybe you have a point entity inside a brush?
Give us the full compile log just in case.