Serial3 uses pin 14,15 and I2S2 uses pins 2,3,4,5,33 so they should not conflict in software or hardware.
My only guess is perhaps the GPS antenna may be too close to signals like MCLK and BCLK. If used indoors, perhaps the GPS antenna gets a very weak signal. Perhaps simply turning on those clock signals is creating small electrical interference which disrupts the weak GPS signal.
Please understand without seeing the complete program and photo of the hardware wiring the best anyone can do to help is blind guessing. If you want better help, please give enough info so anyone could reproduce the problem. But if you can't share that much info, at least let us see. Without seeing, only blind guessing is possible.