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You might check your verison of django-mssql, I believe 1.7+ isn’t supposed to have this issue anymore.
Try running the following against the database:
alter table [user] drop constraint [UQ__auth_use__F3DBC5726EFED139];
drop index [UQ__auth_use__F3DBC5726EFED139] on [user];
And rerun manage.py migrate.
Drop Constraint Failed – unable to drop index with ALTER TABLE DROP CONSTRAINT
Source:stackexchange.com