Why couldn't Philip beat the hell of the Infected?

[Thaliur]

Didn't Philip say he felt weird when he encountered the blueish cloud in the excavation site?

what part is this? overture or black plague? or is this now requiem?

If it happened, it happened in Overture. I'm not sure about it though. It might also have been something like "Better not get too close to this" or similar. I have to play it again to confirm.

Didn't the infection come from the save points? Or was I not paying attention?

The artifacts appeared earlier, you might be right about them being the source of the infection. At least they might have helped it along.
But I'm still pretty sure the blue haze was in some way connected to the Tuurngait.