Let me preface this by saying that this isn't to beg for others or the author to help, but to archive this problem for future reference.

In short, I've noticed that sometimes the vassalage policies for when the AIs use them such as the naming designations or the species related one, it doesn't get properly filled in when the game is saved, making it look something like the following:

{
key=subject_ver_ruler value=subject_ver_ruler_them }

{
key=subject_ver_government value=subject_ver_government_allowed }

{
key=subject_ver_policy value=subject_ver_policy_restricted }

{
key= value=subject_ver_species_policy_restricted }

Note the blank where subject_ver_species should be with key=. This has happened twice so far for me.

This would make the save essentially corrupted until it's filled in again, which is really simple and easy since the error.log pointed me to this problem.

Now I'm sure this is just a matter of my 100+ mods messing things up and it's not on the the author for this problem, but if someone else is having this sort of problem, try checking your game's savestate file when you open the .sav as a ZIP. And check your error log if it gives you something like

"Unexpected Token =, near line; 12345678