I bought plastic storage boxes at Target for $8 each. They are about 6" high and hold about 50 cupcakes. I lay cardboard on the bottom so they don't slide around much. I like the plastic boxes with lids because they help keep the cupcakes fresh. In the cardboard boxes I notice cupcakes dry out faster.
Unless you purposely stuck it on the fondant or cake, which I doubt anyone would do, I can't see how it would end up in the cake and go unnoticed. I would probably freak out too, but I'm sure it'll be fine, let us know what happened.
I found the tips on this link very helpful, http://*********.com/frosting-icing-etc/buttercream-meringues/italian-meringue-or-mousseline-buttercream-or-imbc. Also, I usually take the butter out of the fridge after pouring the sugar into the meringue, let the meringue mix for 20 mins, then add the butter 1 T at a time. If its still too soft refrigerate in 10 minute increments. Add color last.
You can try this calculator.
One more thought. I have a brand new kitchenaid mixer that I believe runs too fast. The stir speed runs more like at speed 6. I mixed it for the recommended time in the recipe. If it is running too fast, can over mixing be causing the problem?