此处的 affecting its operation 以及前面的 flashing on their consoles 都是动名词短语,不是分词.
本句中的 affecting its operation 是对 flashing on their consoles 进行补充说明的并列动名词短语,也就是说,第二个动名词短语 affecting its operation 前面省略了与上文重复的逻辑主语 a blue light.
a blue light continuously flashing on their consoles,和a blue light affecting its operation 都是动名词复合结构.动名词复合结构在书面语中,逻辑主语常用每次所用个（a blue light’s）,但在口语中,用作宾语的动名词复合结构的逻辑主语可以用主格代替.因此,如果罗嗦点儿说,这句话可以改写如下：
Some users complained about a blue light’s continuously flashing ontheir consoles,that is to say they complained about a blue light’s affecting its operation.(有些用户抱怨控制台蓝色信号灯不停地闪动,也就是说抱怨这种信号灯影响它自身的运行)