We can't really give you a one size fits all answer, it could be a number of things. We need more info. I don't own an 05-09 Mustang, but maybe somebody who does knows of some common issue that could be checked first?
'03 Mach 1 5spd
Fully forged Manley rods/pistons, Cobra crank, ARP hardware, 8.5:1, Procharger P1SC w/ intercooler, AFM power pipe, 60# injectors, 03/04 Cobra tank with dual fuel pumps, Kenne Bell Boost-a-Pump, O/R X pipe and Flowmasters, Exedy stage 3 clutch, Steeda Tri-Ax, Front and rear upper + lower control arms, Ford Racing springs, Bob Monks tune 448 rwhp @ 9 PSI