This answer is not linked to the examples cited in the question, and my purpose is not to criticize anyone but to address the topic itself, which is the core of talmudic study in my opinion.
To be respectful toward the words of wise and intelligent persons demonstrates that you really believe that they are chachamim. May be that they already did think about your kashia.
To ask your kashia against is a duty. To think "I have a better pshat" is ok. But to think that they did make a great mistake may be a problem. You need to understand why they didn't say your pshat.
To be convinced that the chacham did not understand the sugya is a symptom of superficiality. The chacham is really a Chacham, so you cannot decide in one second that you know. his process of thinking. Particularly when the text of the chacham was already studied by dozen of genreations of Talmide chachamim.
this trust trust in chachamim is fundamental in judaism, and simply in way to learn rabbinic works, to be persued that peoples like Rashi or Rabenu Tam, Rishonim and great Acharonim have a lot to teach us about Tora and Chochma.
The name of the website is "mi yodeya", this name outlines the importance of our desire to know what chachamim did say and think. If you have even a little quantity of contempt, you cannot spent energy to understand chachamim and cannot reach a high level of learning.
Criticism is appropriate with a right and good taste. We need a censorship against rude criticizm toward chachamim because it can induce error in the approach for beginner members. We know that in holy books there are a lot of rude statements, Raavad on Rambam, Rashba in Mishmeret Habayt, ..etc... but here there is not comparable situation. In a great percentage, rudeness has to do with bad midot.
A great Talmid Chacham told me about a very great rav who wrote a book on hilchot Nidda. This rav discussed about one of the sugiot with the Chazon Ish. He said "the Chavas Daas in this sugya seems to be against the pshat and we see that all Rishonim seem also clearly against this Ch. D.". The Chazon Ish told that the Chavas Daas is also a sugia. I.E. to understand the chavas daat on the sugia is also a part of the limud of the sugia. A chacham feels that to try to understand the Chavas Daas is also to try to understand tora.