The following set of steps will result in the time field being incorrectly set. You can see an example of this if you use the Cashier Closing doctype as it has two time fields in it.
1/ Enter a value in the time field (From Time) by using the time popup control.
2/ Move out of the field to another field.
3/ Go back into the time field (From Time) and manually change the time to another time.
4/ Move out of the time field (From Time) into another field.
5/ move back into the time field (From Time) and you will see that the time field is reset to the value you set it to in step 1 when you used the time control to set the time.
The issues seems to be that the time field control does not reset its value to the new value you manually typed in in step 3 and the value from step 1 is then reinserted into the time field from the control as soon as you enter the field.
This is a bug in the time field operation and I have experienced it everywhere the time field is used.