I don't know about the black pepper grain. I get some of those sometimes but not with that "density".
The strange edge of the tree trunk is in my hazardous opinion a problem of "registering" between two scans, meaning your scanner makes a two-pass (or multiple-pass) reading but than the software does not match exactly the two images. That means the hardware is not suitable for this kind of double-pass reading. If you use VueScan you should repeat disabling "Input - Multi exposure".
As a side note, I don't understand how that house can have shutters which are smaller than the window they are supposed to shut, it's the first time I see something like that.