He's still in his middle school uni in first chapter flash forward. There's been two years of timeskip to fit those scenes into, and the latest installment is first day of high school, so he spent those two years as still a middle school student.
No, what I mean is that in the first chapter he was targetted from some organization or government, someone discovered his powers and wanted him in a way or the other, and he was wearing his middle school uniform, but now after the time skip his uniform is different but it doesn't seems like he got found out, only have some local delinquents bothering, I'm guessing he got found out after helping the exorcist against some monster and his fighting style is unknown and people with power want it.
What I was saying is the mangaka made a mistake and gave him the wrong uniform in the flash forward.