When Chazal declared that "from the day after the Shabbat" means "from the day after the festival,” they did not mean this as an interpretation of the verse in Vayikra; rather, they meant it as a halakhic ruling.
Chazal taught that "from the day after the Shabbat" means "from the day after the festival". Chazal's interpretation was accepted by all of the commentators, but it is difficult to ignore the fact that this understanding seems somewhat forced.
It is possible to say that when Chazal declared that "from the day after the Shabbat" means "from the day after the festival,” they did not mean this as an interpretation of the verse in Vayikra; rather, they meant it as a halakhic ruling, by virtue of the authority of the Sanhedrin to decide the beginning of the count on a particular date, although the Torah makes no such stipulation.
At times, discrepancy between the peshat of the verses and midrashei halakha, stems from practical considerations. These considerations were viewed as important by Chazal, and therefore some of their midrashei halakha were intended to serve these purposes.
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Edited by the HaTanakh Site team