So, the chossid was troubled. What does this mean? Did the earlier generations commit aveiros, chv"sh?
Tzemach Tzedek explained that we are sent into this world to make it a dwelling for G-d it by uniting it with G-dliness through the mitzvos given to us which we use to manipulate the material matter (e.g., eat kosher meat; make parchment for mezuza, tefillin or Seifer Torah out of cow skin; light wax or parafine candles for Shabbos, use wool to make tzitzis, etc., etc.). When we do the mitzvos, they activate the “sparks” of holiness present in all matter.
Those things in which the sparks are accessible are kosher. Those in which sparks are not accessible and thus cannot be elevated are treif. To identify which things are kosher and which are treif, we are given signs (e.g., the simanim of kosher animals). The problem is, however, that in earlier generations Jews were able to elevate sparks more freely than in the later generations. That is why, finished Tzemach Tzedek, the number of chumros increased to safeguard the Jews from consuming such products and in such circumstances in which Jews would be unable to elevate the sparks in these products (making consuming them, from spiritual perspective, not too different from consuming the opposite of kosher, chv"sh).
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Then there is a similar story of the Maggid not eating in the house of Baal Shem Tov. How could this be: a chossid not eating in his Rebbe's house? The answer is that Baal Shem Tov followed a more meikel shitta on shechita of meat (or some aspect of its preparation), since he was able to elevate the sparks in a meat prepared according to this shitta, while the Maggid was not on such a level of holiness.