Latley ive been having problems doing flyes with heavier weights, seems like my right shoulder (lateral head to be exact) starts aching, any ideas as to why this happens? and any suggestions on what to maybe replace flyes with? 

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Originally posted by Prince
I agree, going to deep on flyes puts a lot of unnecessary stress on the shoulders.
You could also try switching to dumbell presses rather than flyes.
Do you do dumbbell flyes every chest work-out? If so, try alternating every other work-out with something different.