If your exceeded time is not being counted, there are several possible reasons:
Please turn on the "Count exceeded time" option in Settings.
This feature is designed to count the extra time spent without opening Forest/using other apps after your planting is finished with the screen locked. If your screen was left on, or if your turn it on to check Forest right after the planting time ends, there will be no "exceeded time" counted.
The exceeded time is only counted until your total planting time (originally set time +exceeded) reaches 120 minutes. That means if you set to plant a tree for 120 minutes, there will be no exceeded time counted.