How MySQL Queries and Questions status variables are calculated?
I answered an old question like this Feb 25, 2014 : Questions since MySQL Startup

In that post, I described how everything MySQL executes to retrieve info is a question. I also mentioned how a billion questions is no big deal (See my ServerFault post 1 billion mysql queries in 24 days? Can something be wrong?)

Here is the difference


Queries : The number of statements executed by the server. This variable includes statements executed within stored programs, unlike the Questions variable. It does not count COM_PING or COM_STATISTICS commands. 
Questions : The number of statements executed by the server. This includes only statements sent to the server by clients and not statements executed within stored programs, unlike the Queries variable. This variable does not count COM_PING, COM_STATISTICS, COM_STMT_PREPARE, COM_STMT_CLOSE, or COM_STMT_RESET commands. 


You should go through the MySQL Documentation and read up on all Server Status Variables.