2006 Honda TRX 250 2 wd won't start by key starts by pulling electric shift doesn't shift error code is 6 flashes from the 1st gear indicator light Question is WTF over?

Your indicator is telling you that you are not in neutral and it will not engage the starter until you are, if the machine is in fact in neutral, or if the clutch is depressed then the sensor that detects it is bad or needs adjustment. the failsafe is the system that keeps you from starting the vehicle in gear.

Here is a list of the codes
1 flash, euc (writing and recording circuit) , probable faulty part ECU

2 flashes ES shift switch system (up and down) probable faulty part, shift switch, related wiring harness, or ECU

3 flashes,angle sensor system, probable faulty part, angle sensor, or incorrectly installed,related wiring, or ECU

4 flashes,gear position switch system, probable faulty part,gear position switch or related wiring or ECU

5 flashes,ECU motor driver circuit, probable faulty part,ECU

6 flashes, ECU fail safe relay circuit, probable faulty part,ECU

7 flashes, ECU voltage convent system, probable faulty part, ECU

8 flashes, angle sensor system, probable faulty part,angle sensor, or control motor, or related wiring, or ECU

9 flashes, angle sensor system, probable faulty part,angle sensor(short or open), or related wiring , or ECU

10 flashes, ignition pulse generator system, probable faulty part, ignition pulse generator or related wiring

11 flashes,speed sensor system(vehicle speed), probable faulty part speed sensor or related wiring or ECU

12 flashes, gear position switch system, probable faulty partgear position switch or related wiring, or ECU