JC, my initial impression on reading your post was 'Jeez, this guy sounds like he worries too much'.
Are you confident in your own ability and knowledge of procedures? If so, stand up for yourself confidently, whilst maintaining a respectful manner, when these issues come up.
If it's just a question of personal preference or style, defer to the Captain if you're comfortable doing that, or express your disagreement, again respectfully, if you're not.
Have you discussed this kind of thing with your peers? Do they find the same issues arise with the same guys? If so, it can be a relief to find 'it's not just me.' If not, perhaps you're being overly sensitive and need to find a way of not taking things so personally.
Apologies if I've misinterpreted your comments.