Wife has left and filed for divorce

[Hoju]

Why did you not call MIL or W first about keeping S for the day before asking for the day off?

Aside from that in the future just make sure everyone is clear on pick up and drop off times.

If you want understanding, try to see it from your W's point of view (whether you intended it or not). She gave you an inch by letting you keep S over night and you took it upon yourself to try and take an extra day out of it. I can't imagine how hard it must be to give up your son while he is crying begging to stay but right now you need to focus on baby steps and building trust with your W for your sons sake regardless if you are able to R or not.