Don't think it should conflict, of course unless you don't have a mod that allows you to have multiple followers.

Who said that? :) You can get almost any two follower mods to work together if you follow the instructions. There are already videos on YT of Inigo and Sofia following players around and I think Sofia is on her own seperate follower system so it really shouldn't be an issue.

I Have both mods and the only issue is that Sofia spends most of her time insulting cats with inigo staying in the same tent.

Let me answer it in the straightest and most direct way possible. No.

Hmm, I did have this one issue with attempting to marry Sofia and everytime Inigo was with me the game crashed. Until I eventually got rid of him then it went through successfully, Shortly after that I went to the Riften Jail and got him. Another weird thing that happens is if I get them both ebony bows inigo will just stop using his and switch to the default hunting bow. (He is using a regular ebony bow not the special one he comes with but I have no idea about that)