If you find that your questions are not being received as they were intended and they were asked with the proper deference (כבוד רבך ככבוד שמים), perhaps you need to ask your question of authorities who are willing to address it, or are comfortable saying they don't know the answer - but may research it. Or, you can ask your question here where you have a decent chance that someone can answer your question. And on this web site, most people are pretty civil.
I personally have not experienced pushback when asking questions in a respectful tone unless the person being asked somehow felt intimidated by the question.
Also, as Fred pointed out, the resolution to your question may be extremely complex and beyond the reach of a novice. You need to appreciate your shortcomings which you may be able to overcome over time with additional studying. (Try explaining the proof to Fermats conjecture to anyone but an expert!)
On a personal note, many years ago I asked a world renowned halachik authority about a difficult passage in one of the Achronim. He agreed with my question. When I asked him if the Achron was wrong he simply responded that I did not have to learn that passage. That Gadol taught me that one can disagree with humility. I have often found that when I am sure I am right, I discover that I overlooked one trivial point which changes everything.
A Note About Respecting Authority
In any discipline, if you have a question regarding the position stated by a recognized authority in the field, it is somewhat rude and arrogant to assume that your question is a disagreement; it is much more likely that you missed some basic point than you have a legitimate point of contention.
Suppose you were a patient being wheeled in for an emergency operation and you disagree with the world renowned surgeon although you have not been schooled in medicine. Would you refuse surgery based on your own self declared expertise or would you defer to the world renowned physician?
In Torah, even more than in other disciplines, one must approach the discipline with humility and recognition that questions should be labelled simply as questions, not as disagreements.
At the same time, I believe, we must be open to all kinds of questions and not be afraid to ask any question. Judaism is a religion that embraces understanding, comprehension and depth and we should encourage discussion and debate as much as possible because only through questions can we grow in our understanding.