No, it doesn't taint or weaken the spell in my experience.
It helps to know it is a two color before using it, the best way to tell is to scrape a bit off the bottom of the candle.
Also if you are inclined you can split the candle down the middle of the wick, not an easy process, and use the candle as a double color one. In the case of the aforementioned candle, it could be used as a red and a white at once. This gives you two candles, once split, to use in different ways.