The Italian outfit found itself at the centre of suspicions about its power unit last year, as rivals pushed the FIA for a number of technical clarifications regarding engine usage.
The responses, as well as comments made by team people and drivers, left Ferrari facing difficult questions at times.
Reflecting on the engine saga in an exclusive interview with Motorsport.com, Binotto said that the situation at the end of last year simply exposed an area where his team was not strong.
"I think that it was maybe showing one of our weaknesses of the season," he said. "We are not good enough in polemics, and there are people who are stronger than us - even in using the media to put pressure on.
"So it is something that we need to understand how to do better, and to better act in the future, because that's part of the overall balance of a season."
Although the focus on Ferrari's engine performance proved the gains the Italian manufacturer had made, Binotto said he did not take any compliment from the fact that rivals were baffled about how the team had done it.
"No, not really," he said. "For me that is more polemics, finger pointing. Which in the end is about putting pressure or extra activity, because you need to reply to the interviews or reply to whatever has been questioned.
"I think it has been a distraction, and something we have been living with – and that is part of the experience. I will always say we are a young team, and being a young team we are facing new situations."
But, Binotto was clear that praise needed to be heaped on Ferrari's engine department for the way in which it had turned around a difficult first year with the turbo hybrids in 2014 to become the benchmark last year.
"I'm very pleased and I know it's not something that happens in a single season," he said. "So when we started in 2014 with a new format, we were a lot behind our competitors, and it has been a long push to challenge them."