I don't know about the timeouts, they seem a bit random at times to me.
As far as subbing in your backups with 48 seconds to go though, that would be due to your stamina. Your coach will generally try to have the best players on the court so if your starters are too tired then the fresher backups might be seen as the better options at the time.
In short, i would be training stamina this offseason ;)