Yeah, you're doing too much weight if you're feeling it mostly in your shoulders. Your muscles have a prioritizing system in which if one group isn't strong enough to counter whatever resistance it meets, it will 'recruit' other muscle groups. For the two you mentioned, shoulders are the primary recruits. When your pecs and triceps can't handle the bench press by themselves, your body naturally uses the front and back shoulders and upper back muscles to help. If those muscles are feeling stressed, lower the weight in 10% increments until you clearly feel it working pecs/triceps (depending on grip). Same goes for dumbell flies.