The Gresini Ducati rider crashed in the hour-long afternoon practice at Le Mans and struggled for pace through to the chequered flag.
His penultimate flying lap in the session was thwarted by a yellow flag, before a mistake while fastest through the first sector on his last effort consigned him to 13th and a place in Q1.
Marquez says this was the first Friday practice since jumping on the Ducati where "it was difficult" for him and says his problems stem from a lack of feeling from the rear of his bike.
"This is the first Friday it was difficult, and the other Fridays were quite easy, pace was good, was easy to be in Q2," he said.
"But it's true that it's the first Friday we struggled more and it can happen.
"So, now it's time to react and try to understand what we did, where I struggle more on my riding style and try to improve for tomorrow.
"I'm struggling because I'm pushing too much on the front because I don't feel the rear. So, we need to understand how to feel better on the rear.
"This bike especially you need to feel a lot or you need to take a lot of potential from the rear. If not, you will struggle, so it's what happened today."
Marquez's crash at Turn 12 in second practice was the first he's had on the Ducati that could be blamed on overriding.
"Today was the first crash for overriding," he said. "You can see the image, I was fighting against the bike. I was not smooth enough, I was not clean on the lines and in that crash, I leant too much.
"I was struggling to keep the lines and then I leant too much. So, we need to understand well and try to understand tomorrow the way to improve."
The Spaniard tried a set-up direction in FP1 that proved effective, but suggests his Gresini team may need to revert to his standard settings for Saturday after his struggles in second practice.
Asked if there was a big difference between his two bikes following his crash, he said: "No, it was very similar between first bike, second bike.
"Was a big difference compared to this morning. This morning, we tried one thing and we decided to go in that direction.
"Now we will have some question marks and then maybe we need to make a step back and try to understand better for tomorrow, because it's true that this morning I go out in the first run and I feel OK, was the best run maybe on the riding style and I was smoother.
"So, let's see what we need to do."
He also batted away suggestions that the rumours surrounding his future were acting as a distraction at Le Mans.
"I'm already 13 years, 14 years in MotoGP," he said. "So, I don't feel that pressure. [It's] the first Friday that we struggle, and this can happen and now it's time to react.
"I don't expect to struggle here in Le Mans, but it can happen. So, we need to understand where we are losing and what we need to do."
