When your plants get to the point where they should die, they turn into a dirt pile instead (not always, but in most of the time). They are supposed to die if they're not nurtured enough, which includes fertilizing them, however if you queue fertilizing with the same type of fertilizer, the game won't actually fertilize your plants leading them into decay. It's a messed up feature of plants decay. There's also one cause that is entirely base game and that is the problem with queuing up the 'fertilize' interaction.

One of them is a Seasons specific bug (allegedly the one that should be now fixed, but who knows if it actually is), the other is due to Eco Lifestyle (that one can be 'fixed' by disabling eco footprint).

There are more things causing this exact bug.