Not a practitioner, just another interested person who studies Zoroastrianism, but I'm guessing you're looking at something like this and seeing that the Gatha Ahunavaiti begins at Yasna 28. This is not an original numbering system for the Gathas themselves. It just denotes where they appear in the Yasna, the part of the Avesta most comparable to a Christian liturgy. That's also why there is a gap between the end of the Ahunavaiti (Y34) and the beginning of the Gatha Ushtavaiti (Y43), there are other parts of the Yasna in between those readings, mostly the Yasna Haptanghaiti (Y35-41), which happens to be the only other part of the Avesta composed in the same Old Avestan dialect as the Gathas. The Gathas and the Haptanghaiti are right in the middle of the overall Yasna.

That said:

Is there segments missing? Or was it originally like that.

There are almost certainly missing Gathas, as well as missing parts of many other sections of the Avesta. The surviving Five don't really paint a complete vision of Zarathustra's faith on their own, appear to describe several disparate points in his life, and are clearly not enough to account for a lifetime of preaching and teaching, let alone the multiple lifetimes of his immediate followers who would have composed their songs and prayers in a similar style. Some Younger Avestan parts of the Avesta and later commentaries even seem to reference Gathas or Gathic-style verses that no longer exist.

There are multiple historical accounts of how and when some or all of these may have been lost. The most famous is associated with Alexander of Macedon, aka Eskandar the Accursed in Middle Persian tellings of the story, but other instances are associated with one of the Parthian kings named Vologasses, the Arab conquest of Iran, and even just the general failure over time to maintain the portions kept as oral tradition (a major point in the 3rd Century CE Letter of Tansar ).

That's to say nothing of the other parts of the Avesta in addition to the Gathas that were also lost. Most "complete" editions of the Avesta will have a section of "Fragments" near the back that includes Avestan texts that don't survive in any complete form and don't traditionally fit into one of the other major sections for this reason.