1) Ch. 17, v. 6: "Al pi shnayim eidim o shloshoh eidim yumas ha'meis lo yumas al pi eid echod" – By the testimony of two witnesses or three witnesses shall the guilty person be put to death he shall not be put to death by the testimony of one witness – a) Since we know that one witness is insufficient even for money matters (Dvorim 19:15), why does our verse repeat this by capital punishment? b)If two are believed here, why bother telling us that three are also believed?
2) Ch. 17, v. 7: "Yad ho'eidim ti'h'yeh bo borishonoh l'hamiso" - The witnesses who testify to the guilt of someone who has transgressed a sin that deserving of the death penalty are the ones who execute the sinner. What is the rationale for this ruling?
3) Ch. 19, v. 19: "Va'asisem Lo Ka'asher Zomam La'asos" - The gemara Makos 2a derives from our verse that the Torah requires that the witnesses give sufficiently specific testimony which could make them liable to be refuted by other witnesses who could say that the first ones are false by virtue of not having been at the location where they claim the situation took place at the time they testified it took place, commonly called "imonu heh'yi'sem." If witnesses don't open themselves up to this risk, they are invalid.
It seems that this ruling makes it impossible to ever have acceptable witnesses. If the first set of witnesses requires the possibility of being refuted by the second, then the second can only be accepted if it can be refuted by the third set, and so on. Eventually we will run out of people, so then the last set will be invalid. This will create a reverse domino effect as the ones before them will likewise be invalid, all the way back to the first witnesses. How can we ever have acceptable witnesses?
4) Ch. 19, v. 19: "Kaasher zomam LAASOSE" - The mishnoh Makos 5a derives from the word LA'ASOSE "v'lo kaasher ossoh", that only when the sentence has not been executed and the witnesses are found to be false in a manner called "hazomoh", that others testify that the earlier witnesses were not present at the time and location which they claimed they saw the act done, do we carry out reciprocal punishment. However, if the sentence was irrevocably carried out, the false witnesses are not punished.
This obviously deserves an explanation. If they are punished when nothing was actually done to the falsely convicted person, surely when the sentence was carried out, and they have brought about actual damage to an innocent person (lashes, death, etc.), they surely deserve to be punished.
5) Ch. 20, v. 20: "Rok ho'eitz asher TEIDA" - When we have a doubt if a Torah prohibition applies, we apply the dictum "sofeik d'Oreisoh l'chumroh," when in doubt regarding a Torah-level law, we are stringent. However, there is a disagreement between the Rambam and the Rashboh if acting stringently is required by Torah law or if by Torah law one may be lenient, and it is only a Rabbinical decree to be stringent. According to the opinion that "sofeik d'Oreisoh m'd'Oreisoh l'kuloh,' that by Torah law one may be lenient, why does the Torah say that only a tree which YOU KNOW is not a fruit producing tree may be cut down? Even when one has a doubt if it produces fruit, he would also be permitted to do so by Torah law.