clocks from PLL to megafunction sdc

Your generated clocks don't have any targets or a relationship to the source clock (defaults to -multiply_by 1). That's why you're getting the warning. As mentioned, just use derive_pll_clocks.

derive_pll_clocks and derive_clock_uncertainty should be placed in the file after the create_clock commands.

Also, what are you trying to achieve the the set_max and set_min_delay timing exceptions? If you are trying to represent phase shifts with them, that that is incorrect. Just remove them and use derive_pll_clocks.