The Team Chest progress will only show the Keys earned towards the next Chest level. It doesn't reflect the total amount of Keys earned during the event.
For example, in the screenshot below, it shows the team has earned 37 Keys towards Chest level 2. This doesn't include the 50 Keys your team earned to reach the first Chest. Therefore, in total your team has earned 87 Keys.
If you still believe your team is missing Keys progress, please let us know.