MDN claims that:
The comma operator evaluates both of its operands (from left to right) and returns the value of the second operand
In the context of a function call, the comma is used to separate parameters from each other. So what you're doing is passing a second parameter to alert() which gets silently ignored.
What you want is possible this way:
alert((1,2));
The extra brackets form a parameter on their own; inside them you can use the comma as an operator.