We all know Kiyoshi missed the first half of the year because he was undergoing rehab due to his injury against Kirisaki Daīchi High in the final match of Prelims the year before.
However, on rewatching the Episode 8 of Season 2, where the flashback of the previous year's journey and Kiyoshi are focused on we see that even before number of times in the episode Kiyoshi is looking down on his legs.
The most specific scene however is ~15mins into the episode, just after Hyuga compliments Kiyoshi on his dunk, we see Kiyoshi wincing and see his leg is quivering. This seems like a stretch that he injured his leg twice in the match. More probable (my theory anyways) he was carrying this injury before the tournament and didn't tell others because he didn't want the team to pull out without him in the first year itself.
Tl;Dr - Was Kiyoshi injured before his match against Kirisaki Daīchi High or it is canon he had another injury?