You use the PA4/PA5/PA6 pins for ISP programming. You also use those pins for normal SPI operation unless you've remapped them to the other set of pins. See section 17.5.4 in the datasheet for details on the REMAP register as applies to SPI.
No major issues. A few things give me pause there: *The decoupling cap appears to be on the rear of the board. Why? Put it on the top, you have the space. No need to make the paths to your decoupling cap longer than they need to be for no reason. * I'd pull up reset with a 10k not 100k - at 100k, why bother? The on-chip pullup is stronger than that. * Why two 100uf electrolytic caps? I don't see a compelling reason for more than one. * If possible, you want all SMD parts on one side (for manufacturability)* Why not use a ground plane on both sides?