Rather than, "How can these things be", the response of Nicodemus is more appropriately, "How is it possible for these things to come to pass?" In other words he is not disbelieving but wondering how it is possible. And while the Master does say to him, "Ye (you all) do not receive our Testimony-Witness", it still does not mean that Nicodemus never understood because he clearly did and that is shown by his words, actions, and deeds, both later in the same Gospel account, (John 7:50-53), and at Golgotha, (John 19:39-42). Moreover the He and he are the Amen-amen in this passage, and that is why the Master says "we" and "our" in this same context, (which I will highlight below), and Rev 2:18 combined with Rev 3:14 informs the faithful as to which one is the Son of Elohim and which one is a Son of Elohim:
Yohanan 3:1-36
[01] Moreover, (during the same week of the feast of Pesakh Matzot from the previous chapter), there was a certain man from the Perushim, his name Nikodemo, Archon of the Yhudim:
[02] This one came to him by night, and said to him, Rabbi, we know that you are a Teacher come from Elohim; for no one can do these signs which you do if not immo·El, (El is with him).
[03] Ι̅H answered and said to him, Amen-amen, I say to you, If one is not born from above the same cannot see the kingdom of Elohim.
[04] Nikodemo said to him, How can an old man be regenerated-reborn? can he enter a second time into the cavity of his mother and be regenerated-reborn?
[05] Ι̅H answered, Amen-amen, I say to you, If one is not regenerated by Water and Spirit the same cannot enter into the kingdom of Elohim, (thus the answer is, Yes-amen, one must go back into the cavity of his mother, that is, mother-covenant, and relearn all things: for Yerushalem above is our mother-covenant, Gal 4:22-27).
[06] That which generates from the flesh is flesh; and that which generates from the Spirit is Spirit.
[07] Wonder not that I said to you, You must be born from above:
[08] The Spirit blows wheresoever He wills, and you hear His voice, but you have not known from where He comes and to where He goes: thus is every one being generated out of Spirit.
[09] Nikodemo answered and said to him, What makes it possible for these things to come to pass?
[10] Ι̅H answered and said to him, You are the Teacher of Yisrael and do not know these things?
[11] Amen-amen, I say to you, We speak that which we know, and we testify of that which we have seen; and our testimony you do not receive, (for He and he are the Amen-amen).
[12] If I told you earthly things and you believe not; how shall you believe if I tell you heavenly things?
[13] And no one has ascended into the heavens if the one who is from the heavens has not descended: the Son of Man.
[14] And just as Moshe lifted up the Seraph in the desert, in the same way must the Son of Man be lifted-up-exalted:
[15] That all who put their trust in him may have life aionion.
[16] For in this manner Elohim so loved the world, that He gave His only begotten one of a kind Son; that all who put their trust in him should not perish, but have life aionion.
[17] For Elohim sent not the Son into the world to judge the world; but that the world through him might be delivered.
[18] The one trusting him is not judged; but the one not trusting is judged already because the same is not trusting in the name of the only begotten one of a kind Son of Elohim.
[19] Moreover this is the judgment; that the light is come into the world, and men loved the darkness rather than the light because their works were evil.
[20] For anyone practicing wickedness hates the light, and does not come to the light, lest his works should be reproved.
[21] But the one doing the truth comes to the light, so that his works may be made manifest, that his works are engaged with Elohim.
[22] Amidst these things Ι̅H and his talmidim had come into the land of Yhudah; and he was wearing through the time there with them, and immersing.
[23] Moreover Yohanan also was immersing in Aenon, next to Saleim, (that is, Shiloh), because there was much water there: and they came and immersed:
[24] For Yohanan was not yet cast into prison.
[25] There came up therefore a mutual disputation of the talmidim of Yohanan with a certain Yhudi concerning purification.
[26] And they came to Yohanan, and said to him, Rabbi, he who was with you on the other side of the Yarden, he of whom you have testified; behold, the same is now immersing and all go to him!
[27] Yohanan answered and said, A man can receive nothing if it is not given him from the heavens.
[28] You yourselves bear me witness that I said, I am not the Meshiah, but that I am sent before in front of that one.
[29] The one having the bride is the groom; but the friend of the groom, who stands and hears him, rejoices greatly because of the voice of the groom: this therefore my joy is fulfilled.
[30] That one must increase, but I myself must decrease.
[31] The one coming from above is over all; the one being from the earth is of the earth, and of the earth he speaks; the one coming from the heavens is over all:
[32] What he has seen and heard, of that he testifies, and no one else will receive his testimony:
[33] The one therefore accepting his testimony has set his seal that Elohim is true.
[34] For the one whom Elohim has sent speaks the words of Elohim, for He does not give the Spirit by measure:
[35] The Father loves the Son and has given all things into his hand.
[36] The one faithfully trusting into the Son has life aionion; but the one not faithfully trusting into the Son shall not see life, contrariwise, the wrath of Elohim abides upon him.
