This was a problem in AE CS6 that I have complained about before. It is not nearly as bad in AE CC, but it's still there. Unfortunately it can be difficult to replicate with consistency. It may have something to do with the conversions between "time" and "frames".
The problem occurs when you have a sequence of layers (each layer taking up a single frame) that is precomped.
For example, this expression can cause problems:
thisComp.layer("frame controller").effect("Slider Control")("Slider").value*source.frameDuration;
This is abstracting the time-remapping to another layer with a Slider Control. It then takes the slider value (which represents frames) and converts it to a 'time' value. I have found this to cause unpredictable results in CS6 and CC. Sometimes it shows the correct frame, sometimes it doesn't.
However, if I modify the expression as such:
thisComp.layer("frame controller").effect("Slider Control")("Slider").value*source.frameDuration + source.frameDuration*.5;
The result is always the same, and correct. Here I am telling it to look at the 'middle' of the frame, rather than the 'start' of the frame.
I hope this is helpful in some way. I wish Adobe would fix this.
I will remind you that this problem has never occured in all previous versions I have used. I am fairly confident it is related to the new image caching system introduced in CS6.