Official comment
The question mark means the system is guessing the % completion based on the best available information. A user cannot enter the "?" manually. An example would be if a task is estimated to take 20 hours of work, but the actual effort put in is 21 hours. The task SHOULD be complete, so Clarizen will put 100? in the % completion. The ? indicates that the system does not know for sure, perhaps the task is running behind and will now take 25 hours. The best way to remove the ambiguity is by populating the remaining effort as well. In the same example of 20 hours of estimated work, if you put 21 hours of actual effort and 4 hours of remaining effort, the system will display 92%... which is much more accurate than 100?. If the task should be complete, marking it complete will remove the ?. Also the ? does roll up and adds ambiguity to all of the parents. The sooner you can remove the ?, the more accurate your plan will be.