Question: I have **Cisco Catalyst 2960-s** switch and I want to configure *three Vlans* (A; B; C)

I want to : 

* *Allow* traffic between A and B
* *Allow* traffic between A and C
* *Block* traffic between C and B

or if there is other method to permit/deny access between switch ports.

Answer: 
When we test failure scenarios we start by removing individual wires/fibres, then whole NICs/HBAs, then servers, then switches - i.e. small to large - simply because if the platform can't handle the small then testing on the large will be pointless.

That said I can't see any issues with your setup, not as you've explained it anyway.
I more go on the big approach - unplug a server and on the next try storage and on the last one a switch - or in any other order - if the system survives that -> all good. But if you do have a lot of time (and someone to pay for it), you can try each small problem on it's own...

Tsg