The calculations of time are based on a number of factors in the print settings but can sometimes the settings affect each other and result in a compounding effect. For the moment our time calculations are going to be off from the realistic time until we are able to find all the different reasons for the variations. I have seen the same thing in almost every printer I have supported in the past including the Zortrax M200, Up Plus (using up software 1.7x), ect. It takes some time and is not super important so this adjustment is always one step behind actual print stopping bugs.
As for the software not canceling the print correctly, this is something we may need to take a look at. The printer, as long as it is still connected to the computer, should have stopped after it reached the inserted line of code to stop the printer. This could take a few seconds to a minute if the G-Code command is quite long for the operation it is currently on. If you are needing to close MatterControl to get the printer to stop then I would ask what version of MatterControl you are on. It seems that one function may be causing all the issues noted relating to this and updating MC or reinstalling it after wiping out the AppData folder may be in order.