Here's another way to look at your wife and her actions. In her mind, she views you as an authority figure (father, uncle, whatever). So when she sees you and your children having fun, she becomes resentful and jealous. Why? Because "dad" and the kids are having fun and she doesn't get to have fun like they do. Don't be surprised that at some point, she will become best buds w/one of the children. They tend to select their best bud based on the child that goes along w/whatever they want and doesn't challenge them. If you want to see some of what your wife may be doing, visit HaWho's threads. Her h has been jealous and sometimes resentful of her two sons. Why? Because HaWho and her sons are living their lives and she is focusing her attention on them. Her h wants attention to, but doesn't know how to go about it as an adult.
As for being late to pick up your son. She's testing your boundaries and authority. If she does it again, gently remind her that the agreed time is such and such. You don't have to tell her that you have anything planned, but stick to the agreed time as much as possible.
Again, she's "teething in her own way", which means she's testing you in some areas. Keep your cool, but you can get your point across over in a nice way w/o sounding like you are cracking the whip at her.
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.