The release numbers of different products provided by MathWorks are assigned depending on the need felt by the developers as and when the developers at MathWorks feel that there is a major change in that product. That is why the numbering of different products differs from product to product.
Answering your question specifically the R2016a had a major change in MATLAB but was not a major change for Simulink
However, with the base product package, you get all the latest compatible products. So even though you feel that the version numbers don’t match, they are still the latest products.
The changes brought to the main products that are MATLAB and Simulink can be seen in the following links:-
https://www.mathworks.com/products/matlab/whatsnew.html
https://www.mathworks.com/products/simulink/whatsnew.html
