Do protein supplements have any side effects?
Not at all. But depends on what brand you are using. If it is pure protein then it has no side effects. If it contains creatine or any other substance which may cause side effects then it maybe harmful. But same as creatine or any other supplement you need to drink more water even if you are eating more meals in a day then also you need to drink more water.
If you are drinking sufficient amount of water with your whey protein then it is even more safer than milk.
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One more thing to remember that you should know daily limit of protein you need. If you are working out or going to gym and want to develop muscles then you need 1gram protein for 1 pound weight it means if your weight is 150 pounds then you need 150 grams of protein. If you are not doing any exercise then you only need half protein from your body weight per pound. If your weight is 150 pounds and you are not doing any intense work then you only need 75 gram protein, Which can easily be taken by 4 to 5 meals daily.