So I have been playing around with the animation features in Krita and there is one thing I haven't been able to figure out yet.

When I try to copy a selection on one frame and paste it to another frame it creates a new layer instead of pasting to the frame intended.

I'm not sure if I'm missing something, or if it isn't a feature yet.

Really hoping someone can help me out!

I had the same problem. Pasting into the active layer or frame is really not possible.
Usually you can paste to a new layer and merge down but this would paste into every animation frame of the underlying layer.

I have found a workaround using a stamp brush:
You can use the clipboard as the brush tip for a simple default brush.
( Here is a nice tutorial from David Revoy: https://youtu.be/fgA4BcO3Nq8)
This needs just a few clicks once you know how it works.

However I hope the developers will find a better solution to this problem.

perhaps it would be a nice solution if the transformation tool had a feature to use the clipboard as source. This does not necessarily need a checkbox- just use the clipboard if nothing is selected. And it is obvious that you are working on the current frame or active layer - transform tool always works like that.
If this seems too obscure there could be a menu entry that invokes this paste operation and jump back to the previous tool after pasting.

I'm working on a longer animation right now and it is really not intuitive to get parts of one frame into another using the easiest available method I have found so far : creating an empty layer , copy frame to this new layer by dragging, transform the desired part and merge down.

Yup! This is a very needed function when animating digitally!

I'm not quite remembering right now how it works in Toon Boon Harmony or Tv Paint, but we just need the same function as it works on those software. I hope it is not something complicated to set up!