When trying to update the database with the second migration it will fails becouse it will try to create the already existing table "public"."__MigrationHistory".

This are the Package Manager Console commands executed to get the current code:

• enable-migrations -ContextTypeName MultipleMigrationsSchemaBug.Dal.UserContext -MigrationsDirectory:Migrations\UserContextMigrations
• Add-Migration -configuration MultipleMigrationsSchemaBug.Migrations.UserContextMigrations.Configuration InitialMigration
• enable-migrations -ContextTypeName MultipleMigrationsSchemaBug.Dal.BookContext -MigrationsDirectory:Migrations\BookContextMigrations
• Add-Migration -configuration MultipleMigrationsSchemaBug.Migrations.BookContextMigrations.Configuration InitialMigration

To get the exception from the Package Manager Console:

• Update-Database -configuration MultipleMigrationsSchemaBug.Migrations.UserContextMigrations.Configuration -Verbose
• Update-Database -configuration MultipleMigrationsSchemaBug.Migrations.BookContextMigrations.Configuration -Verbose

To get the exception from the console application just run it

Note: the error is generated becouse the migration executed this psedo code

if table "dbo"."__MigrationHistory" not exists
then create table "public"."__MigrationHistory"

Note2: if i explicit set the schema of MigrationContext (as described in this link https://msdn.microsoft.com/en-us/data/dn456841.aspx) it works (to try it add the compilation symbol WORKAROUND)