In order to ensure your pushups and squats are counted, follow these steps:
Turn on the volume/ringer of your phone
Press "start" on the mission
Put your phone in your back pocket or waistband with the long side of your phone aligned with your spine (NOTE: if you are wearing high waisted leggings, make sure the phone is below your waist)
Go slowly and listen for your phone to say "squats or pushups detected" (NOTE: if you do not hear this, then your reps will not register)
Each time you pass an interval of 3, your phone should say the number you are on (ex. "6", "9", "12", etc.) If you are having trouble, split up the missions in smaller sets of 10 to 20.
Once you have done your desired number of squats or pushups, slide the button at the bottom of the screen and you will see how many you completed.
Check out this article for more details on how to maximize counter-performance.