Brian Hoyer and the 49ers’ first-team offense didn’t exactly come crashing to the ground during Monday’s practice. But it also wasn’t the smooth-running machine that had been on display in previous sessions. Maybe it was because the unit was rusty coming off a player’s rest day on Sunday. Maybe they were overconfident after so many sharp practices. Maybe they were merely working on some of the less glamorous aspects of the playbook.

Monday’s low? It came during a “backed up” situation, one in which the offense was snapping the ball in the shadow of their own end zone. Hoyer and the rest of the quarterbacks apparently were working on their hard counts. They certainly were effective at drawing penalties … but mostly from fellow offensive players. There were at least three false-start fouls, with Kyle Shanahan sending the second-team offense off the field after an infraction.

“The offense was — I don’t want to point the finger — but they were kind of struggling with the hard count today,” defensive coordinator Robert Saleh said.

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Reuben Foster received plenty of attention Monday — including here — after he practiced with the first-string defense. But the team’s other first-round pick, Solomon Thomas, also had a strong outing. Thomas is playing left defensive end with the second-string unit behind Tank Carradine and, as expected, has been stout against the run. Thomas also had been getting some first-team repetitions on nickel downs — he moves inside to defensive tackle in those situations — when DeForest Buckner was out. Buckner, however, returned to practice after missing some time last week with a sprained ankle.

“Solomon is starting to show up,” Saleh said. “Again, we’re going to have fresh bodies rotation in and out. So, if being a starter is important to a D-Lineman, if they want that first play we’ll talk about that. In the end we’re trying to get a good rotation going, where they are fresh and rolling. Where at the end of the day they may look like they have equal reps. But, in my mind they’re both (Thomas and Carradine) starters.”

Foster wasn’t the only rookie playing with the first-string defense. Undrafted safety Lorenzo Jerome continues to take advantage of Jimmie Ward’s (hamstring) and Jaquiski Tartt’s (ribs) injuries. Jerome, who made a number of interceptions since the spring, had three big “thuds” on offensive teammates: running backs Matt Breida, Raheem Mostert and Joe Williams. The thump on Williams put the running back on his back and drew chirps from the offensive players.

“He’s an instinctual football player,” Saleh said. “Sometimes I look at the tape and I’m like, ‘I don’t know if you can do that, bud.’ But he always ends up in the same spot. He has a good feel, and again he’s a rookie and he’s going through and he needs all the reps, and he needs to see it over and over again. He’s been doing alright.”

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Everyone keeps waiting for Jeremy Zuttah to make his move and challenge for the starting center role. That hasn’t happened yet. Yes, Zuttah gets worked into the first-string offense every now and then. But the bulk of the first-string reps continue to go to Daniel Kilgore, who likely will start there Friday against Kansas City. In fact, it was Tim Barnes, not Zuttah, who got most of the first-string snaps Monday that didn’t go to Kilgore. In those situations, Kilgore played left guard.

Joshua Garnett, the team’s top choice at left guard, was at practice with his left knee in a plastic sleeve. He will get more tests on the knee, but the 49ers are optimistic he won’t need any type of season-ending procedure. Zane Beadles took most of the first-team repetitions at the position.

Hoyer nearly was intercepted early in practice on a throw to tight end George Kittle. Safety Eric Reid jumped the route and broke up the pass. Later, Dontae Johnson grabbed an interception off a tipped pass from Hoyer that was intended for Marquise Goodwin. Johnson has been strong in the last few practices and likely will start Friday’s preseason opener opposite Rashard Robinson.

Hoyer still had his moments Monday, including sharp throws to Goodwin, Pierre Garcon and Trent Taylor. … Matt Barkley also fired a pass to Taylor that beat tight coverage from nickel cornerback Will Redmond. Taylor also has been getting the most punt-return opportunities and, along with Garcon, Goodwin and Aldrick Robinson, appears to be a lock to make the 53-man roster.

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Aaron Lynch was back in practice after missing two days for the birth of his son. Lynch had two batted passes on Monday … Kittle was back after missing a week with a hamstring strain. … Receiver Louis Murphy, who has been slooooooooowly eased into practice since the 49ers signed him last week, had his most extensive action to date. … Because the Chiefs will wear their home red jerseys, the 49ers offensive players are wearing white this week after practicing in red in every practice to this point. (Yes, I’m confused by that logic, too).

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