I don't know what to do with these extra pins and I have tried to delete them but it says "CAN'T DELETE BUS BIT". Those are some sort of replica of the pin in design, even though their I/O Standard is not set to differential . it can be seen at last in image above.
Can you please check with quartus setting file *.qsf?
It can overwrite the previous assignments.
Please refer the "188.8.131.52.1. Adding Pins and DQ Group Assignments" from the link below,