The pasuk says (VaYikra 23:16) “Tispiru Chamishim Yom”; you must count 50 days from the Korban Omer and then celebrate Shavuos. All the Meforshim ask that Matan Torah actually came out 51 days after the Omer not 50.
Rav Yehonoson Eibushitz in Tiferes Yehonoson answers that the count is based on sun days and not moon days. During the war with Amalek, the Amaleikim figured out based on the stars that they could defeat Bnei Yisroel at night. Therefore the Torah tells us that Moshe held up the sun that night. This battle took place after Yetzias Mitzrayim and before Matan Torah. Therefore one sun day wasmissing for a total of 50 days. Technically according to the moon and the months there were 51 days but the count goes according to the sun giving a total of 50 days until Shavuos just like the pasuk says.
