We have this problem sometimes depending on the clothes- for instance Armani has nice pj's from fufufashions and Linda cuts them high enough that we don't have this problem but I have a hoodie from petco and he will pee on it if I forget that he has it on. Basically I have started just letting him wear his high cut clothes in the house and I save the others for instances where I know he won't be peeing without supervision
I suppose if someone knew how to use a needle and thread they could sew the bottoms up shorter, but ever since an unfortunate situation in middle school home ec where my puppet ended up with one arm I haven't picked up any sewing materials