Gemara Eruvin 89
“Everyone Hears Only What He Understands” Johann Wolfgang von Goethe
תוספות הכא
מתני' כל גגות. גזרה משום תל ברה"ר - אף על גב דקיימא לן כר' מאיר בגזירותיו אפילו במקום רבים כדאמרינן בפ' אע"פ (כתובות נז.) גבי משהה אדם את אשתו שתים ושלש שנים בלא כתובה הכא אומר ר"י דאין הלכה כרבי מאיר דפסקינן לקמן הלכה כר"ש דאמר כולן רשות אחת הן וכותל שבין שתי חצירות דאסרינן הכא לר' מאיר שרי ר' יוחנן לעיל בריש חלון (עירובין דף עז.) ולקמן בפירקין [עירובין דף צב.]:
כתובות ס, ב
אמר שמואל הלכה כרבי מאיר בגזירותיו
And Rav Naḥman said that Shmuel said: The halakha is in accordance with the opinion of Rabbi Meir with regard to all of his decrees
תוספות ב״ק ל, ב
אע"ג דקי"ל (כתובות דף ס:) כר' מאיר בגזירותיו דוקא בגזירותיו ולא בקנסותיו וכן פסקו הלכות גדולות כרבנן דר"מ מטעם זה במעוברת חבירו ומינקת חבירו (יבמות לו:):
The question is why only his decrees, but not his halachos nor even his kenasos (financial penalties)?
My thought based on Gemaras below:
תלמוד בבלי, מסכת עירובין, דף י"ג, עמוד ב
אָמַר רַבִּי אַחָא בַּר חֲנִינָא: גָּלוּי וְיָדוּעַ לִפְנֵי מִי שֶׁאָמַר וְהָיָה הָעוֹלָם שֶׁאֵין בְּדוֹרוֹ שֶׁל רַבִּי מֵאִיר כְּמוֹתוֹ, וּמִפְּנֵי מָה לֹא קָבְעוּ הֲלָכָה כְּמוֹתוֹ? שֶׁלֹּא יָכְלוּ חֲבֵירָיו לַעֲמוֹד עַל סוֹף דַּעְתּוֹ. שֶׁהוּא אוֹמֵר עַל טָמֵא טָהוֹר וּמַרְאֶה לוֹ פָּנִים, עַל טָהוֹר טָמֵא וּמַרְאֶה לוֹ פָּנִים.
On the topic of Rabbi Meir and his Torah study, the Gemara cites an additional statement. Rabbi Aḥa bar Ḥanina said: It is revealed and known before the One Who spoke and the world came into being that in the generation of Rabbi Meir there was no one of the Sages who is his equal. Why then didn’t the Sages establish the halakha in accordance with his opinion? It is because his colleagues were unable to ascertain the profundity of his opinion. He was so brilliant that he could present a cogent argument for any position, even if it was not consistent with the prevalent halakha. As he would state with regard to a ritually impure item that it is pure, and display justification for that ruling, and likewise he would state with regard to a ritually pure item that it is impure, and display justification for that ruling. The Sages were unable to distinguish between the statements that were halakha and those that were not.
תלמוד בבלי, מסכת סנהדרין, דף כ"ד, עמוד א
אמר רבינא והלא כל הרואה ר"מ בבית המדרש כאילו עוקר הרי הרים וטוחנן זה בזה
Ravina said in response: What is the difficulty? But is it not so that when anyone sees Rabbi Meir studying Torah in the study hall, it is as though he is uprooting the highest of mountains and grinding them into each other? Rabbi Meir was a greater scholar than Reish Lakish, so it was fitting for Reish Lakish to speak of him with reverence.
Based on these sources, we can surmise the following: When it came to analysis and logic the rabbis could not follow Rebbi Meir, so could not rule in accordance with him. However, regarding his decrees which were of an obvious and practical nature, they could follow his logic and therefore rule in accordance with him.
This is fascinating because even though they trusted his acumen and BELIEVED he was correct, in order to rule halachically, they had to UNDERSTAND his reasoning in order to have the halakha in his opinion. This idea is supported by a similar statement by the Maharal (Nesivos Olam, Nesiv Ha-Torah 15) had strong criticism against the halachic codes of his day because he felt this would lead to an ossification of the dynamic halachic process:
“We are taught in a Beraisa: ‘The Tanaim (this is referring to the savants who memorized the teachings and not referring to the Rabbical authorities who authored the Mishna) destroy the world. Could it truly mean that they destroy the world? Do they not establish the world (by preserving the teachings)? Rather they destroy the world because the offer halachic rulings from their rote memorized teachings...This means that they adjudicate from their teachings without understanding the basis of their rulings. This is why they destroy the world because they are destroying Torah when they do this, as this is not real Torah. It is only real Torah when you decide based on your intellectual understanding...In our generation it would be bad enough if they ruled from the Mishna, which at least is the beginning of the Talmudic analytic process, but worse, they rule from codes which are not designed to teach Torah but rather to offer halachic guides. This state of affairs is contrary to proper thinking. True, the early authorities such as the Maimonides and the Tur also wrote codes and didn't provide their analysis, but their intention was to show the halacha they arrived at through the intellectual and analytic process of studying the sources. It never was their intention that a person should rule from their codes without knowing the underlying reason. If they thought that their writings would have led people to abandon studying Talmud and deciding halacha from merely external texts, they never would have written it. It is far better to rule halacha from studying the Talmud even if it is possible that one might rule incorrectly. The scholar only can know what his intellect shows him from his analysis -- and even his albeit mistaken ruling is beloved to Hashem, may He be blessed. The judge only can judge from what his eyes see. This is far preferable than to rule from a composition without knowing any of the real reasons, to be as a blind man who gropes along the path.”
Translations Courtesy of Sefaria, except when, sometimes, I disagree with the translation 
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