After their beloved team lost in Week 1, Denver Broncos fans were fuming at their new coach, Nathaniel Hackett, who had made a baffling decision at the end of a Monday night loss in Seattle.

So how were they feeling after a Week 2 win on Sunday over the Houston Texans? Well, many of them were still fuming.

Hackett, hired by Denver in January after three years as Green Bay’s offensive coordinator, once again puzzled fans with play calling that cost the team a drive — though not the game.

With four minutes remaining in the third quarter, the Broncos trailed the Texans by 9-6 and faced a third-and-1 at the Texans 35. What play might you call there? A quarterback sneak? A plunge with a running back who was averaging more than 5 yards a carry at the time? A quick outlet pass to try to catch the defense napping?

Whatever your choice, Hackett’s decision — a slow-motion sweep featuring a handoff to the tight end — was probably not the best call.

When that tight end, Andrew Beck, got the ball from Russell Wilson, he was already 5 yards behind the line of scrimmage. Texans defenders were coming fast. Nearing the sideline, Beck moved a couple more yards backward, seemed to fake a pitch to a teammate, and was tackled for a 1-yard loss. He never came close to gaining the required yard.

The team’s No. 1 back, Javonte Williams, was available. But the ball went to Beck, a tight end, who was — incredibly — making only his second career carry.

That led to a Broncos 55-yard field goal attempt, which was good … except that it was kicked after the play clock had expired, largely because the Broncos took too much time deciding whether to send out the field goal team. Boos rained down from Denver fans. “I don’t blame them,” Hackett said after the game. “I would be booing myself.”

The 5-yard penalty pushed Denver out of realistic field goal range — though with Hackett the concept of realistic range can vary — and the Broncos punted.

The team also threw away its final two timeouts with nine and seven minutes left in the game. Since the Broncos had a clock problem in their opening-night loss, this week home fans decided their help was needed.

In the fourth quarter many at Denver’s Empower Field began counting down the play clock as a friendly, if sarcastic, reminder to the coaching staff to get plays off on time.

“I guess that was helpful if needed,” Wilson told reporters. “I guess they do that in basketball sometimes.”

Despite holding on to their lead for a 16-9 win, there were other disquieting signs for Denver on Sunday. The team didn’t score a touchdown until the fourth quarter after scoring only one the previous week. Wilson was 14 for 31 for 219 yards, a touchdown and an interception, a comedown from a solid first week and a preseason filled with optimism since his off-season acquisition from Seattle. And the team committed a whopping 13 penalties after being called for 12 last week.

“All I really care about is the cheers at the end,” Wilson said, “because we won.”

It is Hackett’s issues with the clock, though, that were perhaps most concerning, since last week’s loss also featured some puzzling clock management. Trailing by a point with more than a minute left in the game and facing a fourth-and-5 near midfield, Hackett let 43 seconds burn off the clock before bringing Wilson and the offense off and sending out Brandon McManus to try a 64-yard field goal. The kick would have been tied for the second longest in N.F.L. history, but McManus missed it.

“Looking back at it, we definitely should have gone for it,” Hackett said afterward.

On Sunday, even as he reveled in his team’s first win, he acknowledged it had made too many mistakes, saying, “That’s on us.”

“Too sloppy by the offense,” Hackett said. “There were too many things where we just made it hard on ourselves.”

Hackett has only two games under his belt as a head coach. So one might think allowances would be made. But the booing by the home crowd and two weeks of negative headlines are proof that honeymoons do not last long in the N.F.L.

The Broncos host the San Francisco 49ers on Sunday night. They are 2-point favorites. And if there were an over/under on Hackett blunders it would probably be about 1½.