Arduino uno PWM CTC mode - strange behaviour on interrupt
This isn't the only ISR in the Arduino, there is at least the one counting millis. Counter 0 overflow ISR is not as short as yours, so every 1024us it'll cause some jitter (or as in your case, skipping the edge and basically inverting the phase). It'd be also several clock cycles delayed (against HW generated signal). Pushing and poping the registers into the stack are the deterministic delays, but the latency between setting the ISR flag and calling the ISR routine depends on currently executed instruction (some of them takes 2cycles, and there are also longer ones). 

There is not much time to do anything else either. Your ISR might take less than 20 cycles, but you only have 64 cycles (ISR is called at 250kHz rate so it generates 125kHz signal).
So if anything else prevents your ISR to be called (another ISR, disabled interrupts), you can miss them, as there is only one interrupt flag.

If you want the same waveform on pin 7, just use a wire and let the pin mode as INPUT.

BTW: You don't have to use PORTB = PORTB ^ _BV(PB7);, the PINB = _BV(PB7) toggles PB7 without read-modify-write access.