1) The Tosafot Yom Tov (Masechet Shabbat chapter 7 mishnah 2) writes that this follows suit with the Mishnah in Makot chapter 3 mishnah 10 which also states that the number of lashes the criminal receives is 40 minus 1. This in turn is based on the verse in Devarim 25:3 "He shall strike him 40 times - he must not add on!". The Sages learnt that when the Torah said 40 blows this really means 39. Since we now know that 39 is a special number in the Torah connected with Makot, Chazal also, when they told us that the number 39 is also special because this is the number of Avot Melachot on Shabbot, phrased this in a similar way to the Torah itself, that it is almost 40.

2) The Tiferet Yisrael on the above Mishnah in Masechet Shabbat #25 explains based on the question and answer of the Ran. The Ran (page 31b in the Rif pages on Masechet Shabbat paragraph beginning v'Hamotzi) asks why the Mishnah in Shabbat does not also count carrying 4 amot in the public domain as one of the avot melachot. He answers that since we know that the 4 amot surrounding a person is considered as his personal domain it follows that if someone carries 4 amot this means that he is carrying out from his own domain into the public domain. If so, this action is included in what the Mishnah does state that one of the Melachot is to carry out from one domain to another. So the Mishnah says that there are 40 melachot because this is how many there are according to the question of the Ran but since according to the answer of the Ran there is one less melacha, this is why it says "minus 1".

3) Tiferet Yisrael also cites Lechem Shamayim who answers that if one counts the melacha of "Techumin" - walking outside the city boundary on Shabbat - there are in fact 40 melachot. However even according to the opinion that Techumin is a Torah prohibition, nevertheless one is exempt from bringing a sacrifice if one transgressed it. Therefore the Mishnah says "minus 1" because even though there are 40 Torah prohibitions, there are only 39 prohibitions that require a sacrifice.

All the best

Dovid Bloom