Reading the air in the Japanese workplace

You might have heard of the Japanese phrase "Kuuki wo Yomu / 空気を読む" which literally translated means "reading the air." The phrase refers to the social skill of being able to understand things that are not actually being said from the atmosphere or based on facial expressions and other nonverbal signs from the people around. You often hear from foreigners that they have trouble with this as some things, that maybe every Japanese person understands without them needing to be said, are not as obvious for foreigners who grew up in a completely different culture. 

Have you had experiences with this at your workplace in Japan?

I have had some experiences with "kuuki wo yomu"  that I would sort in that kind of category, although I am not sure if that is appropriate.

At my first workplace in Japan, a lot of my colleagues used to do overtime. On the contrary, I managed to finish my work on time, most of the time, and as the company had a weird policy in regard to overtime payment (the first hour of overtime each day was unpaid overtime) I did not have an incentive to work overtime and so left on time where possible.

As I kept my task deadlines I did not see any problems with my behaviour. Before coming to Japan I had heard that in Japan it can be considered rude to leave work before your boss does, however, in the office I worked at my boss was usually not actually at the office but working at home or visiting clients, so I figured that would not apply here.

After a few months in the job, my boss said that they wanted to talk to me and I was told that several colleagues had been complaining that they were doing overtime and I was not. My first reaction was that I did not understand why that would be my fault. If there was a discrepancy of workload causing that, it would be the fault of my boss not having distributed the work evenly. However, it seemed that my colleagues were not looking to decrease their workload.  Instead, my boss told me that they wanted to me to ask them before leaving if there was something I could help with. As I wanted to keep the job and wanted to try being nice I did that, however I never got any tasks from my colleagues and still left on time most of the time.

Until this day I am not sure what problem my colleagues had. As after my boss talked to me nothing really changed but I never got any similar complaints at a later stage.

I assume that in that situation I was not able to read the air correctly.

How would you interpret this situation?