P.S. This is on Skyrim Special Edition on the Xbox One, and I am using multiple mods, to be frank, I can't be bothered with going through every single mod and figuring out which mod is causing the problem.
It seems that you're describing a normal issue. Some weapons are just so large that they "melt" into your armor/body.
Many games have this same problem, to some degree.
Weapons added by mods might have more extreme issues, especially if also used alongside modded armor, because they were not designed to be used with each other.
Unless the weapons is literally stabbing through your entire body, it's probably just a issue you have to ignore.
If it's extremely bothersome, you'll need to pinpoint which mod the weapon/armor is coming from.
Um.... weapons clip through everything. It doesn't matter what game you're playing.... (My GODDESS you should have seen the clipping in WoW when riding.... Didn't matter WHAT weapon one used...) There's not much you can do about it. I play stealth archers exclusively, and while I don't have the clipping through everything with bow and quiver... I have the OTHER problem - where bow and quiver are out in left field somewhere, seemingly not with any relevance to the girl by whom they're supposedly being wielded. As in - they seem to be attached to some body in some OTHER universe entirely.
Not in game right now. If I remember in the morning I'll get a screenie and post it. Mostly - I just do my best to ignore it....
Yeah, that sounds normal.
As the above replies state, many games have this issue.
It's not really a glitch, it's just that the meshes have not been fitted alongside each other very well.
Developers do their best to make sure weapons look good when sheathed, but they usually settle for one set location for all meshes to sheath. Most look fine, but others will float far away from your body while some melt into your body.
I believe Skyrim has mods to fix this problem. I suggest asking in the mod forum for "Sheath fixes."
Well, you pretty much have to change out skeletons to get sheath fixes, which can cause all sorts of other problems. I *think* I've heard the XPMS32 skeleton is pretty good.
You may just have to ignore it as it's common among many games. As Serethil already mentioned it's called "clipping." You'll find clipping happen with various things including sheathed daggers "stabbing" the leg while sneaking. Maybe dig through some mods to see if someone provided a solution for this already.