49ers’ Shanahan denies having any troubles with Lynch

49ers coach Kyle Shanahan refuted a report Tuesday there’s trouble brewing between him and general manager John Lynch that could eventually lead to a breakup of the team’s leaders.

Shanahan told NBC Sports Bay Area that the Bleacher Report story claiming he and Lynch “aren’t in lockstep as far as the vision of the offseason and the future of the franchise,” and he doesn’t trust Lynch’s decision-making is “complete (expletive).”

Matt Miller, Bleacher Report’s draft analyst, said his sources within the 49ers scouting and coaching staff told him the public perception of Shanahan and Lynch sharing the same beliefs on how to rebuild the storied team simply isn’t accurate.

“Shanahan wants to scheme and develop players while not being bothered with the player evaluation process,” Miller wrote Tuesday morning, “but more and more he finds himself involved while not trusting the decision-making of Lynch .. (who is) not someone with a scouting background.”

Miller wrote he was warned of a potential power struggle between Shanahan and Lynch that could eventually result in the ouster of both Lynch and vice president of player personnel Adam Peters.

Miller said he wasn’t surprised by Shanahan’s firm denial of his story and stood behind his story.

The cardinals also said they weren’t drafting Kyler. What do you want him to say? https://t.co/GNy9ak6ede

— Matt Miller (@nfldraftscout) April 30, 2019

“The Cardinals also said they weren’t drafting Kyler. What do you want him to say?” Miller tweeted.

I don’t despise anyone. Especially not Lynch. I’ve rooted for the 49ers my whole life. I want them to succeed.

But as you mentioned, don’t think anyone can deny that I’ve had plenty of info on them dating back to Baalkes regime. Even had them taking Deebo at 36 for a while https://t.co/KKOgS1WCDk

— Matt Miller (@nfldraftscout) April 30, 2019

It should be mentioned no one is saying there was any disagreement with the 49ers’ choice of Ohio State edge rusher Nick Bosa with the No. 2 overall pick in last week’s NFL draft. Bosa was the consensus top player available.

The 49ers hired both Shanahan and Lynch in 2017, arming them each with six-year contracts, to turn around a franchise that won a total of seven games in two years and fired two head coaches. Despite winning just 10 games the past two seasons, 49ers owner Jed York recently voiced strong support for how well the Shanahan-Lynch tandem was working out.

“I think it’s been interesting to watch these guys really come together and show they are a stronger bond today than what they were two years ago, and it’s only getting stronger,” York said at last month’s NFL owners meeting.