I have encountered these kind of problems. I have seen these kind of issues when working with multiple levels of submicroflows. Only last week I had one where I commit an object pass it to a submicroflow, do some validation where in one path the object needs to be again committed and then this error complaining that the object is not there anymore.
The right sollution would be to create a support ticket if you can reproduce the problem consistently. I could solve it by rebuilding parts in the parent microflow instead of the submicroflow. But with a before commit action you do not have that option.