Hey James,
Hope you are well. This one can be handled by understanding how people think. This isn't a question of method, but almost a case of the "too perfect theory", mixed in with effect selection issues, and understanding your audience. This topic alone could be a book, so I expect you to fill in some gaps here.
This is how it goes - people see an effect that has no connection to it. They see a "look at me" style effect that they don't relate to, so their minds go to method. They come up with a method, and their method is as good as any...because honestly, if they guessed a method...and felt compelled to tell you, it is not the audience mistake, but a misstep you took in the process of entertaining them.
Let's take Sean's saw effect - it is a shock value trick. Not only that, but because we know that it is impossible...and not the "oh my gosh that is impossible" type of an effect, but truly impossible in the sense you would be dead, decapitated, or a government experiment type of impossible - their minds go to method. Vernon said something along the lines of this, "knowing that something was done, is as bad as knowing exaclty what was done" because the focus is on method and their minds percieve an out. GOOD MAGIC LEAVES NO OUTS - IN METHOD, PLOT, the entire thing must looks like magic...but still be possible.
For example, I find bill flloats in close up, not in parlour or stage, will not get good responses - because people know their is a string...they don't think...wow, this guy has the power to float things. Ammar says in the book "Switch" that he realizes people won't believe it is magic, but if they question their senses that it is a moral victory - and I think this is true. People don't think it floats, so their is no magic - because it defies what they know.
However, much other magic, despite our knowledge can look impossible, because even though we know it is impossible, no method can explain it...at least not a commonly known one. Which is why ACR can be so deceptive, despite the simple method. It looks moveless. Nothing a layperson knows can explain it.
Strong magic has to entertain, but it also has to look like magic would - or why are you a magician?
It sounds to me like your effect selection is poor, if you are getting these responses on your Youtube videos and in real life - it could also be that you aren't connecting with your audiences and giving a reason for the magic to happen.
Their is a big difference in the audiences mind in seeing an effect as a trick, and seeing it as a show piece that has justification or a connection to them. This is part of what makes magic an art form - it is not just the deception, but the value of the experience to the audience.
Another way to look at it is like a friend of mine named Andrew Musgrave states, it like this - What superpower are you claiming, and does the method support it? So you are claiming in Saw you can pull a thread through your neck? Does the method back it up? In SAW this is a resounding "no" - listen to your audiences.
The too perfect theory, in short, is a theory that states that an effect can be designed in such that it leads people to one theory, and that is the correct one.
You need to take into consideration many things in magic - not all tricks are good.
This is one of the reasons I can do MANY different coin effects, but 4 professionally...or that some of my favourite card effects to do for me...will never meet the eyes of an audience. You have to think about what it is you are showing them - it has to fool them, and if it isn't...well, you aren't a magician if you don't.
At the basic level - our job is to fool - we then go from there.
I could go forever on this, but I won't - let me know if this helps. In short, if someone calls you on an effect - you either flashed, the method wasn't strong enough, you aren't performing it in a way that allows the audience to take their mind off method - or a combination.
With Saw - it is the middle reason - trust me...and I love Sean.
Good luck with the magic, hope this helps.