I've been having some problems with my animal crossing game play. Occasionally I would see this quick twitching light flash on my touch screen and then it stops it looks like a vertical line. I'm not sure if the hard copy disc is scratched or there's dust in the insertion area? But usually I have no problem with that flaring up sometime, it's just that this one time it happened again my lemon tree had one lemon on the tree, and on the beach where my special hybrids are, some of them disappeared. Now I did have my gates open and people visit and leave, but I think my regular visitors know the rules in my town and I'm not sure if it got stolen or it was the twitchy light flash that caused the content in the game to go missing..? I did look on the interent about whether villagers had anything to do with it but most say they just plant and water, so any thoughts on what you might think it is?
I don't think that line would cause items to go missing. I actually have an answer for both your flower and lemon issues, but not so much the line.
For the lemons, I've searched around online and apparently that's a really rare glitch that happens. Some people have said it looks like there's one but when they shake it, three fall off.
For the flowers, I'm sorry to say but they've likely been stolen. Just because you think you know someone and that they won't steal, you never know. I've had friends steal from me before. If you want, I have a bunch of hybrids I can give you for free to replace them!
What you found is correct, they just plant and water. If you plant a hybrid at the same time in the same spot a villager is planting, it may overwrite your hybrid though. It's happened to me before.
Does that light appear on just ACNL or on all your games? It may just be your 3DS and not your actual game. I'll do some more looking around online though.
Whatever you do, DON'T blow in either your game card or DS game card slot; the moisture from your breath will possibly cause more damage to it.
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All the searching I've done about your line issue points to an issue with your 3DS. The only suggestions I've seen have been to turn it off and back on, and if the line is still there, contact Nintendo or send it in for repairs.
