Does anyone know how to fix skin showing through pants?

I don't see anything out of the ordinary from the screenshot you provided above.

 

But regardless if your character's body is clipping with the clothing objects, use simple trainer or skin control to find a matching outfit that will fit well with your character's body shape. 

I see a little skin in between the shirt and pants.  The easiest way I correct that is to open EUP menu while you are wearing that uniform.  Go to Wardrobe and I think it is an Upper Skin that you need to change.  You just have to go through the Upper Skin numbers until you find the best one that hides the skin where it shouldn't show.  If you customized that uniform then you would have to note that new upper skin number and then change that skin number in whichever uniform mod you used (EUP or LSPDFR).  I would think you used EUP.  If you used LSPDFR then I guess you might have made the uniform in your safe house closet.