Rear gear change misses 1 gear
Hard to say exactly what is going on but I suspect the problem is in the cables and housing - either a routing problem or the cable is sticking.

Inspect the cable run and ensure there are no kinks and the housing is inserted in frame bosses properly.

Pull the cable out and clean it, lubricate and re-install (can be hard of the tip of the cable is frayed). Even better, replace cable and housing which is relatively inexpensive.

Re-adjust the derailleur. Start by rechecking the high and low limits. Start the indexing on the smallest sprocket - that way you know you won't have the problem of the derailleur arriving on the smallest sprocket with on click to go.