I don't have FNV or TTW installed at the moment, so recounting from memory entirely.
You open up FNVEdit. Have only the SIG esp ticked. The master files will load up on their own.
Once the mods finish loading, click on the "+" button in front of the mod esp.
Numerous entries will drop-down.
Find the levelled items entry. Expand it with the "+" button. You will see a big-ass list of stuff the mod adds. Look for the name of the item that might be causing an issue select it. Press delete.
The first time it will give you some time to make peace with the fact that you are changing the mod, and will give you a chance to rethink your life choices. Delete the SOB afterwards, and everything that looks bothersome to you.
homemade pipebombs, Metal Cooking Pan and wingsticks had issues with them, as far as I remember. So did several of the new added jumpsuits (the red rocket one, I think). Also, for whatever reason the Talon stuff made them turn up naked and with only a granade, a knife, and a flamethrower between them, so I deleted everything to do with Talons from the mod.
There was a bunch of other stuff. I deleted the homemade crossbow, because its model looked incomplete.