“Why do most people pronounce the first two words of the Kaddish as יִתְגַּדַּל וְיִתְקַדַּשׁ when the גר”א demonstrated that those two specific words are not Judeo-Aramaic but לשון הקדש and should thus be pronounced יִתְגַּדֵּל וְיִתְקַדֵּשׁ? (See ס’ מעשה רב.)
Why do most people say כִרְעוּתֵהּ when, as the גר”א demonstrates, the כ”ף should have a דגש? (The word should be כִּרְעוּתֵהּ. Again, see ס’ מעשה רב.)”
Because there are those who are choleik on the gr”a. (I think the yaaveitz, but am not sure.)
Interestingly, the mishna berura writes like the gr”a regarding your 1st paragraph, but not the 2nd.