Breaking include on find when irrelevant columns in the join table

So some of my join tables don't have the same foreign key constraints that `sequelize.sync` imposes. Therefore when I delete an instance, it doesn't delete the corresponding rows from the join table. When this happens, it breaks the include using the join table. 

I should add reference foreign key constraints to my tables but this should not happen. 

Also, what is the best way to add foreign key constraints like the ones created w/ `sequelize.sync` when creating tables through migrations.