It depends on the features you're having problems with. If it's filter through command, then look at the Plugin in question, look at if I'm doing anything crazy which selections, which I'm not, and strip the selection of newlines, which will cause unintended problems.
Scribes asks GTK for selected lines and uses what GTK tells it. I don't think I can do anything better than that at the moment. You're welcome to look in the code and see what I'm doing wrong.
Alternatively avoid using the mouse for selection and you Scribes selection functions, that may help some.