One thing you must understand is you shouldn't ask for approach to a problem. However since your question requires it.
First you should add Tags to the buttons to differentiate them:
button1.Tag = "1";
button2.Tag = "2";
Then in your event handler cast the sender object to your control type:
Button a = (button)sender;
Then check the tag of the button a to add frequencies:
freqArray[Convert.ToString(a.Tag)-48] = freqArray[Convert.ToString(a.Tag)-48] + 1;