The project wasn't with out Problems but because of such strict planning they could be solved. For example one of the TBM's got stuck for months, another issues such as sub contractors delivering fraudulent materials also had to be dealt with. [2]
Although the Swiss part went well there are issues with the connection in Germany and Italy. Some projects in Italy haven't even started yet and one part Switzerland is now paying for just to get the trains through.
[1] https://en.wikipedia.org/wiki/Gotthard_Base_Tunnel [2] http://www.tagesanzeiger.ch/wissen/natur/was-die-tunnelbauer...