Captured nuts or weld-nuts in a welded component like this which is subsequently e-coated, is really common in the automotive industry, seen it myself about a million times. I can see that the internal threads in your nuts are not covered in e-coat, so that doesn't seem to be the problem.
If you haven't done so already, you need to grab some of those bolts and go down to the line yourself and check how easily the bolts thread into those nuts. Check fitment before welding, after welding but before e-coat, and after e-coat. If the nuts are tough to go on the bolts to begin with, you need to go upstream to the supplier and find out what's going on. If the bolts thread in easily before weld but are tough afterward, then something's happening in weld. Distortion, weld spatter, misalignment, whatever. If the bolts thread in easily with your fingers but the assembly process or tooling is having trouble, then that's the problem. Misalignment, insufficient or excessive clamping force, etc.
I'm sure you've already done this. Tell us your findings.
Hitting the bolt with a hammer to try to get the threads to start, isn't doing you any favours.
Someone already touched on this, but please confirm that you are starting both bolts by a few turns before tightening either one of them down, so that the part being installed has a bit of wiggle room for the bolts to align themselves. Also confirm that the part being assembled isn't trying to preload the bolts with a side load in any way. I can pretty easily see how that sway-bar bushing holder could be out of tolerance if the stamping process is off, or if the bushing is tight inside the bracket, leading to its natural hole-to-hole dimension not matching what's welded into the subframe. We like having one of the holes being a smidge oval in order to accommodate misalignment in that direction.
