No you can not efile state returns when you file federal joint and state separate. You have to mail the state returns.
Did you follow this article? If you need to file a Joint federal and separate state returns
https://ttlc.intuit.com/community/using-turbotax/help/how-do-i-prepare-a-joint-federal-return-and-se...
Reading the FAQ it looks like you have to use 3 returns. One to file the Joint return. Then you each need another new return to fill out fake federal MFS returns to do your separate state returns.
