Edinburgh were always in the match thanks largely to the kicking of Greig Laidlaw, who slotted home eight penalties, but tries in each half from Mick Kearney and Robbie Henshaw plus Parks' kicking saw Connacht home.
And after missing out on recording a first hat-trick of RaboDirect PRO12 wins since 2010, Scott was in downbeat mood.
"I'm really disappointed and very frustrated. We had numerous chances to win the game," said Scott.
"A lot of individual errors cost us in the end along with some poor discipline.
"They got a bit of confidence when Dan came back on, they started winning collisions and we were always on the back foot."
Edinburgh return to action against Treviso next Friday and Scott was quick to demand a response from his players.
"A lot of the Italian international players play for Treviso and we need to find some answers come next Friday night," he added.
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