Since 1.10, using plant material to fertalise garden plots has been buggy.
The first two slots will fertalise correctly, however unlike in 1.09, this will use up over 2/3 of the plant material and not leave enough to fertalise the 3rd slot. When you attempt to fertalise the last slot, the animation will stop halfway through requiring you to do the fertalise action twice. Upon completing the second animation on the 3rd slot, the slot will appear to be fertalised, however next time you interact with the plot, such as to water it or add a seed, the plot that had to be fertalised twice with the remainder of the plant material will revert back to being unfertalised but will not allow the player to re-fertalise it, however other players are able to.
The bug is hard to explain using text so please refer to this video: