It seems for (key in from) { ... } in mergeData let them go through.
https://github.com/vuejs/vue/blob/v2.0.5/src/core/util/options.js#L44

obj.length = Math.max(obj.length, key) in set throw the TypeError when the array has own properties. I think it's better to merge all elems and properties from the from array.
https://github.com/vuejs/vue/blob/v2.0.5/src/core/observer/index.js#L189

This seems to be a bug in the VueCharts library, because mergeData should never be called on arrays. This means the library is somehow passing an array as the data option, which is not supported.

The VueCharts library does not pass an array as the data.
https://github.com/vuejs/vue/blob/v2.0.5/src/core/util/options.js#L49
The mergeData will be called recursively. So the function will be called on arrays when the data include array properties.

Here's another example without VueCharts:
https://jsfiddle.net/bdpkrnus/

And I think the mergeData will copy properties from from object's prototype to the to object. Is this by design?

There is indeed a bug in mergeData, but your usage is incorrect: you should not be declaring a prop and a data property using the same key.

After the fix you should see a warning message telling you not to do that.