Will solder layer of via short a trace?
It would only be a problem if copper is touching copper (and if you run a Design Rule Check (DRC) then it will make sure that copper doesn't touch (unless it's the same net name, in that case you intended it to connect)
The solder paste layer does extend to far beyond the footprints (unless you intended to do that), you may have issues manufacturing an assembled PCB or if you have a solder paste stencil produced. The solder paste layer normally extends to the only the pad for most parts.