SQL Server 2014 SSIS Package Ignores Script Task when running as AGENT
That occurred because VS 2015 was built to support only SQL server 2016 and you probably deployed the package under SQL Server 2014 or lower(unsupported versions). 

With the latest version of Data tools in VS 2015, you can chose the targeted SQL server version in the package to allow SSDT to chose the correct .NET libraries used in the script component.

See this link for details