The issues are one part offensive line struggles and another part chemistry with receivers.
The most notable disconnect is between Colin Kaepernick and new No. 3 receiver Stevie Johnson. The wideout admitted this week part of the chemistry troubles stems from his "unorthodox" style requiring time to build rapport with a quarterback.
Kaepernick concurred with that assessment.
"There are times that he's going to make a move on a DB, and you have to be ready because he's also making a move that you have to see," Kaepernick said, per The Sacramento Bee. "So I think that's something where it took a little bit longer just to get used to his body language because he had some unorthodox things that he does. But ultimately his separation is there, he's getting open."
Coach Jim Harbaugh said this week Johnson's spot on the 53-man roster is secure, even though his preseason has garnered just two receptions for 11 yards.
The receiver believes the chemistry issues have already begun to dissipate.
"I would say we're getting close," Johnson said. "I can't say we're completely on. It's only been a couple months. It's getting there. I can't say we're clicking right now but we're getting there."