Just had this issue today, in 2017, no less, and you first noted this issue back in 2015 it appears. Mine was a little opposite, though. My schedule was due to run on Thursday, 3/30, but when I woke up in the morning, it was clear that the yard hadn't been watered. I didn't receive any notifications about this apparent skip, and the watering schedule appeared as though it had actually been watered. This morning, 4/1, two days after the fact, I woke up with notifications that the yard was watered this morning, but when I look in the in the watering schedule, it doesn't reflect that the yard was watered. b It's almost like the application and the controller are on different days of the week.
I'm rather disappointed that Rachio hasn't updated their app in any meaningful way since I first purchased it over a year ago. I've been excited for new features and settings to come out, but I'm beginning to realize that this isn't going to happen until a competitor shows up and gives Rachio some competition and reason to expand their app's capabilities. I'm a data geek and just wish I could set the flow rate of each zone, wish I had the ability to tie in moisture sensors and get zones watered literally as-needed instead of what their algorithm has guessed my yard's moisture level is, etc.
Kind of disappointing, but it seems to be par for the course for what every smart home system is doing these days-- release an app with bare-bones features and then never update it beyond what it was released with. Nest, Philip's Hue, and Rachio are all guilty of this. To give Rachio some credit, though, at least they're not as bad as Nest's app which hasn't added any settings since I first bought the thermostat three years ago.