[Hall of Famer]

Well its not a bug, its the intended behavior. An item with click increment effect can only raise the adoptable's level by 1. If the resulting new number of clicks is sufficent to raise its level further, all you need is to click on the adoptable manually. Each additional click(not by item, but by your regular daily clicks) will raise the adoptable's level by 1, until it no longer meets minimum clicks requirement for next level.

For instance, in your example, using 'honey' on a lv.0 adoptable will raise its level to 1, but with 100 clicks. If you click it, it becomes lv.2 and 101 clicks. Another click will make it lv.3 and 102 clicks. Yet another click will only raise its clicks to 103, but the level remains at lv.3 until it has a total of 120 clicks, the minimum requirement for lv.4 adoptables.