I'm creating this discussion as a way to help anyone who's having trouble getting the mod to work, I'm listing a few fix's you can try out to make the mod the work, although some of these require going into the game's data. Also sorry if there's any broken English or if this doesn't work for you.

Some mods will effect how portraits look, these can range from mods that change every character portrait to just a single character portrait. For example a mod that effects how Isaac looks and changes his portrait, uses it's own portrait sheet and will cause the Yet Another Portraits Mod to not work. To fix these issue find out which mods use their won portraits and disable them.
This isn't actually deleting anything major, but this does require you to go into the game's data to alter some mods. In the first method I, some mods will alter the all character portraits, and if you still want to keep those mods enabled while having the Yet Another Portraits Mod active you're going to have to browse the games local data, go to the mods folder, select the mod folder that's causing the issue, go to the gfx folder, and then go to the ui folder. Inside you should find the mods portrait, then you can either delete it or move it somewhere else. After that the mod should still work, and the Yet Another Portraits Mod will show.