Rashi famously does not usually ask a question, so reading his commentary is a little like playing Jeopardy. “Here is Rashi's answer, what is the question?” But in these examples, Rashi makes clear what the difficulty is.
Extraneous Information
Missing Information
Compare and Contrast
(א) כל עדת ישראל יעשו אתו,. לָמָּה נֶאֱמַר לְפִי שֶׁהוּא אוֹמֵר בְּפֶסַח מִצְרַיִם "שֶׂה לְבֵית אָבוֹת", שֶׁנִּמְנוּ עָלָיו לְמִשְׁפָּחוֹת, יָכוֹל אַף פֶּסַח דּוֹרוֹת כֵּן? תַּ"לֹ כל עדת ישראל יעשו אתו:
(1) כל עדת ישראל יעשו אתו ALL THE CONGREGATION OF ISRAEL SHALL KEEP IT — Why is this stated? Since it says of the Paschal offering offered in Egypt, (v. 3) “a lamb for the house of their fathers” which means that they are to be registered for it by families, one might think that in the case of the Paschal offering offered by future generations this must also be so! Therefore Scripture states: “All the congregation of Israel may eat it” (i.e. any of them may eat it whoever they may be who combine to do so) (Mekhilta d'Rabbi Yishmael 12:47).
(1) ויהי הגשם על הארץ AND THE RAIN WAS UPON THE EARTH — But later on (v. 17) it says. “And the Flood was upon the earth”! But the explanation is this: when He poured down the water at first He made it fall in mercy (gently), in order that if the people would repent, it might prove a rain of blessing; but when they did not repent it became a destructive flood (Genesis Rabbah 31:12) .
Superfluous Information
(1) ויסעו מרפידים AND THEY JOURNEYED FROM REPHIDIM — What does Scripture teach us by again expressly stating from where they set forth on the journey, for is it not already written (Exodus 17:1) that they had encamped at Rephidim and it is therefore evident that they set forth from there?! But Scripture repeats it in order to make a comparison with the character of their journey from Rephidim to that of their arrival in the wilderness of Sinai! How was it in the case of their arrival in the wilderness of Sinai? They were in a state of penitence (as shown by the unanimity with which they encamped before the mountain: cf. Rashi on the end of this verse)! Thus, too, their setting forth from Rephidim was in a state of repentance for the sin they had committed there (see Exodus 17:2) (Mekhilta d'Rabbi Yishmael 19:2:1).
Contradiction
(2) יתרו JETHRO — He was called by seven names: Reuel, Jether, Jethro, Hobab, Heber, Keni and Putiel. ... Hobab is certainly identical with Jethro, as it is said, (Judges 4:11) “of the sons of Hobab, the father-in-law of Moses” and therefore it is correct to say that Hobab is one of his names. But as to Reuel there are some who say that he is not identical with Jethro, but that he was Hobab’s (Jethro’s) father, as may be seen from Numbers 10:29. Then what, according to this view, would be the meaning of (Exodus 2:18) “And they came to Reuel, their father” (from which it would appear that Reuel and Jethro are the same)? It means their grandfather, for children call their grandfather: father. This is to be found in Sifrei Bamidbar 79 (on Numbers 10:29).
Sequence (Out of Order)
(א) וַיְדַבֵּ֨ר יְהוָ֧ה אֶל־מֹשֶׁ֛ה בְּמִדְבַּ֥ר סִינַ֖י בְּאֹ֣הֶל מוֹעֵ֑ד בְּאֶחָד֩ לַחֹ֨דֶשׁ הַשֵּׁנִ֜י בַּשָּׁנָ֣ה הַשֵּׁנִ֗ית לְצֵאתָ֛ם מֵאֶ֥רֶץ מִצְרַ֖יִם לֵאמֹֽר׃
(1) On the first day of the second month, in the second year following the exodus from the land of Egypt, the LORD spoke to Moses in the wilderness of Sinai, in the Tent of Meeting, saying:
(א) וַיְדַבֵּ֣ר יְהוָ֣ה אֶל־מֹשֶׁ֣ה בְמִדְבַּר־סִ֠ינַי בַּשָּׁנָ֨ה הַשֵּׁנִ֜ית לְצֵאתָ֨ם מֵאֶ֧רֶץ מִצְרַ֛יִם בַּחֹ֥דֶשׁ הָרִאשׁ֖וֹן לֵאמֹֽר׃
(1) The LORD spoke to Moses in the wilderness of Sinai, on the first new moon of the second year following the exodus from the land of Egypt, saying:
(1) בחדש הראשון [AND THE LORD SPAKE UNTO MOSES] IN THE FIRST MONTH — The section which appears at the commencement of this Book was not spoken before Iyar (the second month; cf. Numbers 1:1): you learn, therefore, that there is no “earlier” or “later” (no chronological order) in the Torah. But why, indeed, did not Scripture open the Book with this section? Because it implies something disparaging to Israel (Sifrei Bamidbar 64:1) — that during all the forty years they were in the wilderness they offered only this single Passover sacrifice (Tosafot on Kiddushin 38b s. v. הואיל)