When comparing databases, we constantly get the tables with no differences. And final script doesn't have any alter statements.

Ex.: the table
CREATE TABLE SecurityContextXSiteGroup (
SecurityContextId INT NOT NULL,
SiteGroupId INT NOT NULL
)
ENGINE = INNODB,
CHARACTER SET utf8mb4,
COLLATE utf8mb40900ai_ci;

ALTER TABLE SecurityContextXSiteGroup
ADD UNIQUE INDEX SecurityContextXSiteGroup_UN(SecurityContextId, SiteGroupId);

ALTER TABLE SecurityContextXSiteGroup
ADD CONSTRAINT SecurityContextXSiteGourp_FK FOREIGN KEY (SecurityContextId)
REFERENCES SecurityContext(SecurityContextId) ON DELETE CASCADE ON UPDATE CASCADE;

ALTER TABLE SecurityContextXSiteGroup
ADD CONSTRAINT SecurityContextXSiteGourpFK1 FOREIGN KEY (SiteGroupId)
REFERENCES SiteGroup(SiteGroupId) ON DELETE CASCADE ON UPDATE CASCADE;

The other table ("differs"):
CREATE TABLE SecurityContextXSiteGroup (
SecurityContextId INT NOT NULL,
SiteGroupId INT NOT NULL
)
ENGINE = INNODB,
CHARACTER SET utf8mb4,
COLLATE utf8mb40900ai_ci;

ALTER TABLE SecurityContextXSiteGroup
ADD UNIQUE INDEX SecurityContextXSiteGroup_UN(SecurityContextId, SiteGroupId);

ALTER TABLE SecurityContextXSiteGroup
ADD CONSTRAINT SecurityContextXSiteGourp_FK FOREIGN KEY (SecurityContextId)
REFERENCES SecurityContext(SecurityContextId) ON DELETE CASCADE ON UPDATE CASCADE;

ALTER TABLE SecurityContextXSiteGroup
ADD CONSTRAINT SecurityContextXSiteGourpFK1 FOREIGN KEY (SiteGroupId)
REFERENCES SiteGroup(SiteGroupId) ON DELETE CASCADE ON UPDATE CASCADE;

The generated update script:

-- Disable foreign keys

/*!40014 SET @OLDFOREIGNKEYCHECKS=@@FOREIGNKEYCHECKS, FOREIGNKEY_CHECKS=0 */;

SET NAMES 'utf8';

--

-- Set default database

USE client_sol;

--

-- Enable foreign keys

/*!40014 SET FOREIGNKEYCHECKS=@OLDFOREIGNKEY_CHECKS */;