I don't think there were any hints prior to Season 4 about what the Observers really were, and no real indication that they were the source of the ZFT's crisis. I think it was pretty clear that the war that the ZFT was trying to stop was the invasion of the shape shifters.

I'm not entirely clear whether the ZFT story was "resolved" once Olivia met Bell in the prime-universe, thus fulfilling ZFT's purpose and moving into the next phase, or if the whole story arc was dropped in favor of the "Walternate's plan" story that dominated the next two seasons.

In Season 4,

DRJ pops back up and he is apparently quoting the same ZFT propoganda as he did the first time (He recruits Cortexiphan patients for William Bell using "the old words"). Walternate's shapeshifter army has long since stopped being a thread, though,

so I suspect there is much more to the ZFT story than just what happened in Season 2.

Prior to Season 4, my answer would have been pretty straighforward.

There were no hints, from anyone, about what the Observers really were, and no real indication that they were the source of the ZFT's crisis. No one knew who or what they were, while Bell and the other ZFT-ites clearly knew (or thought they knew) what it was they were fighting against. I think it was pretty clear that the war that the ZFT was trying to stop was the invasion of the shape shifters, and we have no reason to believe those came from anywhere but Walternate's science division.

I'm not entirely satisfied with the "resolution" of the ZFT story arc, but in a totally out-of-universe way. I feel more like they took the whole alternate-universe story in a different direction and just dropped the ZFT bit on the floor. But that's just MHO; in-universe ZFT was about the shapeshifters, and those were a weapon of Walternate.

After the past few episodes of Season 4, my answer changes slightly. I still do not believe that the Observers are the source of the ZFT's warnings, however:

DRJ pops back up and he is apparently quoting the same ZFT propoganda as he did the first time (He recruits Cortexiphan patients for William Bell using "the old words"). Walternate's shapeshifter army has long since stopped being a thread, though,

so I think the answer now to your question is "we haven't yet found out exactly what the ZFT was warning about because it hasn't happened yet."