Line intersections are displayed where they shouldn't ?

[ericemc3]

Here is a simplified use case: 2 layers, i simplify and filter the first one, then merge both. And i get a bunch of red dots, many line intersections are signaled that are not relevant.

https://mapshaper.org/?files=https://gisco-services.ec.europa.eu/distribution/v2/nuts/geojson/NUTS_RG_03M_2016_3857_LEVL_1.geojson,https://gisco-services.ec.europa.eu/distribution/v2/nuts/geojson/NUTS_RG_01M_2016_3857_LEVL_1.geojson

-simplify 1% \
-filter "FID=='FRI'" 

The result is OK, i can see the original layer with pale blue strokes (i call it the "shadow layer")

Then -merge-layers target=1,2

results in

It looks like the "shadow layer" is interfering, is still taken into account for the topological/intersection analysis