I, too, enjoyed this miniseries. I especially enjoyed the bits involving the politics between the various Native American tribes.
I believe Squanto was under suspicion because: a) he was clearly lying about Hobbamock agreeing with him when Squanto was urging the trading party to continue on instead of heading back to the fort when they had sprung a leak in their boat; b) his cousin, who was the one with the bloodied head found by the settlers left behind at the fort while Squanto went on the trading mission, said that the Pokanoket and the Narragansett were joining forces to attack the settlers, but when Hobbamock's wife was sent to confirm this with Massasoit, Massasoit stated this was a lie; and c) when the settlers went to rescue Squanto from when he was taken prisoner, Hobbamock found him in a tent completely unbound, which called into question about whether he was actually a prisoner. He also was clearly mistranslating a bit when the Narragansett came to pay tribute to the settlers to try to insult the Narragansett/rile them up (which worked because the Narragansett then sent the settlers a bunch of arrows - a sign of war).
It seemed like this was all an effort to try to get the English settlers to fight. My question, though, is why was Squanto trying to incite a fight in the first place?