Please be cautious when gardening in houses that go over the 250 housing limit through the use of bric-a-brac elixirs. In some extreme cases where a house has more than 250 gardening items, there is a chance your plants could be mysteriously changed into a housing object or disappear completely. While this occurrence is rare, we believe our programming wizards have tracked down the issue and will be fixing it in an upcoming update to the game. In the meantime, please garden with discretion and avoid building new large gardens of over 250 gardening items (remember the soil counts as one item and the plant counts as another) in one house.
I have had this happen to me lots of times where objects in the garden change their names and plant likes will disappear quite frequently. Usually going inside the house and coming back to the yard will correct this. The only bad thing is that as long as the likes are "disappeared", your plants do not show the likes as being available. I do have the max bric a brac elixir (350) for my red barn farm, and yes, this issue seemed to happen a lot when I had 3 full gardens (about 166 plants) going at the same time.
I have also had some non-gardening effects as well. I place mannequins and if you have a bunch of plants it can affect those as well. Sometimes I cannot make any changes to the mannequin, adding or removing items from it. If I wait until the plants elder and harvest them and wait a day it will clear the issue. Then I can make any changes to the mannequins and at that time replant the seeds. It will however happen to the mannequins again once the seeds have been replanted.
While they are chasing that issue, please have them look at this:
There are times when I harvest a plant that drops seeds of itself, that I get a seed for something unrelated. Example: recently i got a white laffodill instead of a couch potato when I harvested the couch potato. It's also happened to my magmapeas. It's fairly rare, but it has happened more than once.