I hate to speculate since real info would come from people who worked there and surely prove me wrong.

But you asked for it so I'll do it anyway ;)

Looks like with Clark's background he had already built things for Amazon that are more profitable than what Petersen has built.

This could be a fundamental seed for disagreement that could arise at any time.

One thing's for sure, Clark is capable of making profits happen and that's what he was there for, I am confident he would not fail but I think all were disappointed at how long it might take.

Meanwhile, Petersen decided to divert his attention from Flexport, to becoming a VC, maybe it's a good opportunity and would be possible to get an earlier return from someone else's company more so than his own.

Then on his own it seems like Clark might have wanted to accelerate progress by leveraging more of their war chest, he presents incredibly low risk compared to alternative executives, but it just shortens their runway if things can't be turned around in time.

As can be seen Clark's growth strategy has been replaced by circling the wagons for now.

I've seen things like this happen and it's actually kind of embarassing for a company if they can't prosper more with a leader like Clark than they can without.