"Dubious" refereeing decisions caused Jersey's according to head coach Harvey Biljon.
Jersey led 15-13 at half-time, but 18 unanswered points in the last 25 minutes saw Scottish win.
"There were a couple of very dubious decisions early on which gave them the field position to be able to get those scores," Biljon told BBC Radio Jersey.
"We felt we were doing the right thing at the right time but we didn't get the reward we should have," he added.
Jersey slipped to eighth place in the Championship as a result of the loss, and have now lost their last two league games, having previously been on a club-best run of four games unbeaten.
"I will definitely be able to find positives in this game but I need to find out the interpretation of a couple of things," Biljon added.
"We came with a gameplan, we stuck to task, we were very unlucky not to get the rewards we deserved, and London Scottish are a very good team. We played pretty well for 80 minutes."