Months before an unmanned SpaceX rocket exploded on the launchpad during a routine fueling exercise in September, a NASA advisory committee had raised red flags about the company’s intention to use the same procedure to fuel future boosters carrying astronauts.

On Monday, the committee met and issued further strong warnings about the potential safety hazards of the way entrepreneur Elon Musk’s Space Exploration Technologies Corp. plans to fuel rockets before they are slated to transport U.S. crews into orbit.

The...