The solution lies in removing the explicit definition of the public schema in your classes.

So if you have this in your bar class

bar_id: Mapped[Integer] = mapped_column(
        ForeignKey("public.bar.id"), index=True, type_=Integer
    )

And in your foo class

__table_args__ = (
    {"schema": "public"},
)

Remove both public statements. Postgres does sometimes not explicitly name it that way and alembic then thinks it is a different FK and tries to recreate them.