What does "Red apples and bottles" mean?
The apples are red and the bottles are red too.
The apples are red but the color of the bottles is unknown.
Which one is right ?
It is perfectly ambiguous. If someone says "there are red apples and bottles in that box over there," one may have [red apples + bottles of any color] or [red apples + red bottles]. I don't even know a way to make a distinction with the tone of voice here; if you care to get more specific, you really have to say more words.
EDIT: upon further reflection, I think with tone of voice/speed you can say
red [slow] apples-and-bottles [fast] to imply both are red, whereas you can say red apples and bottles to imply that just the apples are red.
Written, it's 100% ambiguous.
I would use a comma as in "Red apples, and bottles, were placed over.." for the case where bottles color is unknown, just to tell both cases apart, or either change the order of the subjects to avoid ambiguity
I would say that in most cases "red apples" is intended to be a multi-word unit, and therefore the color would only apply to the apples unless otherwise made clear by the context in previous or following statements that the color is intended to apply to both.
As stated in hunter's answer, it could also be made clear through tone and speed that it implies both - without that specific delivery, however, it would likely be assumed that "red" just applies to the apples. The reason for this is because you, as a listener, hear "red apples" first and create the expected multi-word unit, it already exists logically as "red apples" in your mind and the "and" and anything that follows now has no relationship to the color by the time you hear it.
This is specifically true in situations where the color (or other descriptor) is a common addition to the first word - we often say "red apples" or "green apples" to specify what kind of apple we're talking about. If you were to say "red cans and bottles" the intention would be more ambiguous absent other clues. If the items are particularly similar, then it would be more likely to mean both - "red glasses and bottles" probably means both the glasses and the bottles are red, but you can't be sure..
If you're trying to craft a more clear communication, if only the apples are red, it might be better to say "bottles and red apples", if they're all red then "red bottles and apples" might work (because now the multi-word unit kind of encompasses the whole phrase), but it's probably clearer to say "red apples and red bottles".
If the bottes are of any colour, reverse the order to prevent ambiguity, i.e. "bottles and red apples". If the bottles were also red, repeat red, i.e. "red apples and red bottles".