The 49ers quarterback situation is murky, with quarterback Colin Kaepernick taking limited reps in practice due to injury recovery, and quarterback Blaine Gabbert taking the majority of reps. As detailed here and here, both quarterbacks have a long way to go in establishing themselves as the clear cut favorite to be the starter. There really is no quarterback controversy though, because Blaine Gabbert did not fare all that much better in his 8 games as the starter last season.
Going into this offseason, the 49ers were expected to draft a quarterback that could come in and compete with Kaepernick and Gabbert and the favorites that emerged were Jared Goff and Carson Wentz.