Hi Louise,
My Little one is 9 mths now, but i remember having this question for the clinic when i went back when he was 3mths as i too was concerned, and it is very common to have diff coloured poo, for me as i was breastfeeding and giving him formula at night, this was the reason his poo was yellow and green (ie: green was from formula and yellow was from breastmilk).
Also, it is due to the iron levels in the milk that is causing the colour change.
U have nothing to worry about.