I noticed that when throwing Seeds at it from a distance to finish a completed recipe, the flower pops out but the ingredients and water seem to stay. Easily fixed by putting new water in it or breaking it, but strange nonetheless.

Minor issue.

EDIT: Probably a desync, happens very often though. With the Runic Altar as well (in a slightly different manner, namely when placing things too quickly on it).

Can't reproduce, might be related to poor ping.