How can long-term injured reserve cause a bonus overage?
The most common reason a team ends up with a bonus overage penalty is because it operated close to the salary cap's upper limit the previous season and was forced to put a player or players on long-term injured reserve.
Operating close to the cap with players on LTIR for a full season results in teams operating close to or exactly at the salary cap's upper limit, meaning they essentially finish the season with zero available cap space.
For teams in these positions with players earning performance bonuses, those bonuses are tacked onto their final cap payroll and carried forward as a penalty the following season.
CBA reference: Section 50.10 (d) (P. 226-231)