Does anyone know?

This happen sometimes

Linkage ID : You shot blue when the linkage_id of the portal was set to 0. Then the trigger moved the linkage_id to 1, so the portal that opened was linkage_id of 1, and shooting the blue one would have fixed it.

I fired the portal a second time and it still didn't open so the linkage_id couldn't have been 1

No, you don't understand, if you do open a blue portal with the old orange, then the linkage id stays at 0.

too complicated;didn't bother version: You skipped a room, and shot the blue portal before the orange one was placed properly, therefore linking your blue portal to an older orange portal that never got fizzled because Valve.