Yes that’s because of how the gocontrol controller works (between the firmware and stock device handler it doesn’t comply with the ST requirements a 100%). When you open the device using the app, the ST sets the state to opening and it triggers your automation. If you try to open the garage door manually, the state switches from closed to open because the GoControl garage door controller doesn’t report an opening state to SmartThings, hence it will never trigger the automation.
Try changing your rule to trigger the automation when the garage is open instead of opening. That should fix it for you.
If you have access to rboy apps., you can also check out this enhanced device handler for your gocontrol garage door controller which fixes some bugs in the stock device handler and also adds some features, plus this smartapp which automates many garage door actions: [RELEASE] Garage Door Open and Close Automatically when People Arrive/Leave with Timer and Actions