I had an issue with the holes in the flanges not being even a close fit over the pegs so I filed them a bit. Have I made an elementary mistake early on because they really would not fit at all? Once I could get the pegs to fit I now have the gap. Was I supposed to force them to fit would adjustment because I had squeeze maybe a 3mm and forcing it would have scraped all the paint off. I did try being a bit forceful but it just looked like they were not going to fit at all.
Without seeing your specific kit parts, it's hard to say. Maybe there was a molding problem, maybe you just didn't fit them right. All you can do now is make sure that pylon connection inside the secondary hull is as solid as you can get it. Reinforce it with Evergreen/Plastruct strip - bits of sprue will do if you can carve/sand them to the right shape.