Did the US directly contribute to the spread of these groups by funding Pakistan during this time?

Directly? No. Indirectly? Eh, maybe, if so, then only slightly. There are many, many other factors at play here. Too many to count, really. It's too complex to place blame on one entity or thing. But that sort of goes to the next point:

wouldn't that implicate America as the source of the instability there decades later, in our own time?

The instability there has been ongoing for hundreds, if not thousands of years. Long before "America" was born.

I watched the documentary Bhutto

Keep in mind that documentary is incredibly biased. It's a great documentary, but it's wholly 1-sided. And life isn't black and white. See this piece by the Guardian which talks about the bias in the documentary. They say it's a great documentary, but completely biased towards pro-Bhutto.

Quote from the article:

"But it's hard to ignore the very obvious fact that this is one history lesson which is far from objective; put simply, the film is very pro-Bhutto and very pro-Zardari."