They explained what happened.
Yuki thought it was a tire issue and pulled off the track. He undid his seat belts at that time expecting to get out of the car. The team said no the tire is good bring it back to the pits and he did (not having redone his seat belt, which he did get a slap on the wrist for). They swapped out the tires and redid his seatbelts to send him on his way. As he started going again he said there was still an issue (the team is now saying it was the differential) and he was instructed not to block traffic in the pit lane and find a place to pull off.
Should they have sent him back out without actually checking on the car? Easy to say with the knowledge we have now, but in the heat of the moment during a race and the team apparently not having all the information about the fault? I could see why the decision was made to send him back out.