Any time you weld the metal shrinks in the heat affect zone, which warps the panel and will cause a valley or low spot. You have to stretch the weld/HAZ the correct amount to reverse the shrinkage so the panel has the correct shape again. MP&C has a really good method of stretching welds here:
https://www.bangshift.com/forum/foru...hing-mig-welds
It also looks like the inner bottom may have been misaligned before tacking it in place. Panels like that are best fitted with the door on the truck so you can have the door properly adjusted, then trim the lower panel so that it fits the door opening correctly. Once the inner panel is properly fitted in place, then you can weld the outer skin on. I like to make taller patch panels for door bottoms so that I can more easily reach the back side of the welds to stretch the weld beads, depending on where the inner access hole is.