Hidden colours on objects

Hello all.
Lately I have been having some issues that I have never encountered before working the same way that I have always worked in Illustrator.
Sometimes I will use a different colour for a line while I work on it so that I can easily differentiate it and then change it to the required colour later. I think that sometimes I do this for a whole group of lines and so to recolour them I may select the group or even the layer to get them all and then either use the dropper tool so they match the others or change it manually in the color picker.
But now I am having difficulty where I may change the colour but then it will change visually but will still look the old colour when looking at the swatch on the left. It is so messy to fix it that it has been difficult to find out exactly what has been going on and pinpoint the issue and I cannot replicate it when I try (not sure if colouring the layer effect by accident but I try all that with often no effect. 
Saying that, the design I am working on should only have three colours (a certain grey, white and then Rich Black). Sometimes a 0 0 0 100 sneaks in instead of the RB so to be sure I went to recolor artwork to make sure the only colours in the image are the ones I needed and there is also red. None of the lines appear red so it is hard for me to 'select same' to find out where this colour is coming from.
Does anyone else suddenly have this issue and also is there a way of finding what objects are giving this colur reading without having to select one to 'select same'?

Thank you so much.