John 3:13 is a rather typical and ordinary textual variant in many ways.
It features a common-enough external evidence split: a small minority of manuscripts of one text-type (Alexandrian) with limited versional backing (Coptic) versus the majority of manuscripts backed by the broadest range of versional support, with equally early patristic support on both sides.
Shorter Reading: P66, P75, Aleph, B, L, T, W, 083, 086, 33, 1010, 1241, Coptic versions
Longer Reading: A, Delta, Theta, Psi, 050, f1, f13, BYZ, Latin versions, Syriac versions, other minor versions
What is unusual about this variant is its theology. In the majority of manuscripts the text reads as follows: 'and no one has ascended into heaven except the One descending from heaven, the Son of Man who is in heaven'.
The extra words (highlighted above) seem hard to accept as genuine and original, for they teach that Jesus, while saying these words, was both on earth but also present in heaven. Even for believers with the deepest reverence for our Lord and Master, this seems to be attributing something extraordinary to Jesus, something that we are not comfortable with.
Except that John elsewhere attributes omnipresence to Jesus in his gospel. Thus, in John 1:48, Jesus said to Nathaniel, 'Before Philip called you, when you were under the fig tree, I saw you'. Nathaniel responded by saying, 'Rabbi, you are the Son of God, you are the King of Israel!' Nathaniel's response shows that Jesus didn't 'see' Nathaniel in some natural way - what happened was supernatural. Again, at the end of John 4, Jesus healed the nobleman's son at a distance of some 30km/20 miles, thereby demonstrating omnipresence.
While most Christians are happy to accept that Jesus was omnipotent, and even omniscient (three times in John's Gospel we read that Jesus knew 'all things', which is how we define omniscience), we seem to struggle with the idea of omnipresence. Or, if we accept He was omnipresent, we do not like to think of His omnipresence extending as far as heaven. However, theologically, it is difficult to dissociate omnipresence from the other two attributes. Think of it this way: if Jesus was only able to do miracles upon people he was in immediate contact with, and was unable to do miracles at a distance, then He was neither omnipotent nor omnipresent. We might conclude that His limited presence limited his power too. Similarly, omniscience and omnipresence are associated in Psalm 139, for if God is everywhere, then He knows all things too. Similarly, if God's knowledge were limited, then His power, or ability, or do whatever He pleased would be somewhat diminished, or at least not as effective, for knowledge (as we say) is a form of power. God is a unity, and we cannot separate His attributes - they stand together.
It follows therefore that if Jesus is God (as John's Gospel none-too-subtly tells us), then it should not be so disconcerting for us to accept that Jesus was omnipresent. And that, by definition, means that Jesus was present in heaven at the same time as He was on earth.
In fact, the undisputed text in John 3:13 seems to say as much anyway: 'No one has ascended into heaven except the One descending out of heaven'. If Jesus was the One who descended out of heaven, then it follows that He also ascended into heaven, and John 3:13 isn't talking in the future tense about his 'ascension'.
The disputed text is therefore theologically disconcerting (which may explain why one strand of the evidence omitted it), but perfectly theologically acceptable once we have started thinking the way that John himself wants us to think about Jesus.
John 16:16 has an interesting variant. Here are the two versions:
1. A little while and you will no longer see me, and again, a little while and you will see me.
2. A little while and you will no longer see me, and again, a little while and you will see me, because I go to the Father.
In other words, there is an add/omit variant which reads 'because I go to the Father' at the end of the verse (5 words in the original Greek).