The software did not calculate Federal tax even though I know I owe after doing it all manually. Suggestions?

There is much wrong with this software.  But certainly the fact that after it did the transfer from the CRA it crashed and of course I cannot rerun that process as some flag has been set.  But to the specific question the system did not process any federal tax payable, so I went and did the process manually and of course I owed.  Anyone have this problem?  I am doing it for self employed so a fuller package than the basic