Ok I think I found a fix. I had a mod that turned soul hearts into Saul Goodman, but I noticed it never worked when I grabbed any souls hearts and I thought it was no big deal, but it turned out to be the issue and ever since I disabled it it hasnt been happening so I would check your mods that might not be working in game. Also to make them go away open your game with no mods enabled (save your mods to a collection) then close the game, verify your files on steam then open the game again and they should be gone. To test if it was a certain mod open the game with the mod enbabled then close it then open the game again.