SANTA CLARA, Calif. -- Just minutes after spraining his left ankle at the end of the first quarter in Sunday's loss to the Arizona Cardinals, San Francisco 49ers running back Matt Breida was up and jogging on the sidelines, just hoping he could return to the game.

It's not just that Breida wanted to play. It's that he felt like he needed to return since injuries have mounted all over the roster. Alas, Breida was just another 49er stuck on the sideline.

“If Breida can’t go back in the game, then no one can go back in the game because he works as hard as anyone at that," coach Kyle Shanahan said. "He’s been one of our better players and obviously when he’s not in there it’s definitely not easier.”

Such is life for these banged-up 49ers. This is a team that has already lost starting quarterback Jimmy Garoppolo and running back Jerick McKinnon to season-ending ACL injuries and entered Sunday's game without defensive back Jimmie Ward and receivers Marquise Goodwin and Dante Pettis because of their own ailments.

Even the players who did play Sunday were battling through something as eight of the team's 22 starters had spent at least some time on the injury report over the past two weeks. That included starting cornerback Richard Sherman and 80 percent of the starting offensive line.

To be sure, the 49ers are saying all the right things about the injury bug that they haven't been able to swat away.

“It is just what you have to do," right tackle Mike McGlinchey said. "It is football and guys are going to get banged up. Unfortunately, we have had quite a number of banged up guys in the short five weeks that we have been playing. That is just the mindset that we have had from the top to the bottom starting with (GM) John (Lynch), Kyle, all the way down. That is what we do here. Those are the kind of guys that we have here and that is only going to continue.”

While the injury issues have only served to make this season far more difficult, they are also complicating the bigger picture. The 49ers are a team in the second year of what once appeared to be a massive rebuild. The addition of Garoppolo seemed to shorten that curve a bit but removing him from the equation also exposes many of the roster's other warts.

The Niners are still struggling in many of the areas that figured to be problematic even before the season. The pass rush has been almost non-existent save for defensive tackle DeForest Buckner and the secondary -- save cornerback Richard Sherman -- has endured the type of growing pains that seemed likely when the Niners committed to a handful of young, unproven players to man most of its spots.

Beyond that, the Niners are also seeing a receiving corps that is inconsistent when it comes to separating from defenders and is leaning on players with extensive and/or current injury issues to produce.

Digging deeper into the team's depth chart naturally means a decrease in talent but it doesn't mean the Niners should be having some of the self-inflicted issues that have plagued them, either.

"It’s not hard," receiver Pierre Garcon said. "We know the plays, we know what to do. At the end of the day, it’s run the ball, catch the ball, throw the ball, do the plays the coach calls. It’s not overcomplicated. Everybody in here has played football long enough to know how to adjust to anything that happens on the field."

Five games into the season, we know enough about the Niners to know that they still need plenty of work. The sheer amount of injuries they have suffered from week to week has made it hard to know exactly what needs the most attention.

Perhaps the next 11 weeks will bring better health and more opportunities for the Niners to define their needs. Some of those will remain the same, while others could take a backseat to something new.

After Sunday's disheartening loss to Arizona, Shanahan's message to his team was simple. It focused on curtailing the costly mistakes and focusing on improving one week at a time. A year after opening the season 0-9, the Niners again find themselves in the middle of what looks like a lost season.

"... We put a lot of work into this," Shanahan said. "Every Sunday we come out very confident and we expect to win and we’ve come up short a number of times. I told our team, we would love to be 4-0 right now and we’re not or 5-0. It’s something that is hard to deal with, but it’s something that we all can. We know why we lose each game. Each one has been a different reason, but we’re not going to sit here and just start pointing fingers at each other and chasing a bunch of stuff. You’ve got to look into each game and what it is."