the arguments need to be seperate strings within a list. How you have it, your passing in a list that looks like ["x,y"]. You need your list to look like ["x","y"]
try something like this:
skipList = ['x']
skipList.append('y')
cmds.pointConstraint( 'sph1', 'sph2', skip=skipList )
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This works because your string is passed within a list to the argument.
skip=[myString] is not the same as skip=myString
so you were passing it skip=["x"] which of course works, but you needed to append another string to your list, instead of add to the string itself. which was giving you skip=["x,y"]
Hope that helps